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From: Colin <col...@gm...> - 2020-01-24 21:10:01
|
Hello everyone! I'm pleased to announce a new jbrowse maintenance version. This includes a number of features and bugfixes suggested by the community. Please see the release notes below for details. - JBrowse-1.16.7.zip <https://github.com/GMOD/jbrowse/releases/download/1.16.7-release/JBrowse-1.16.7.zip> - minified release - JBrowse-1.16.7-dev.zip <https://github.com/GMOD/jbrowse/archive/1.16.7-release.zip> - use this if you modify jbrowse source code or use plugins - JBrowse-1.16.7-desktop-win32-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.16.7-release/JBrowse-1.16.7-desktop-win32-x64.zip> - JBrowse-1.16.7-desktop-linux-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.16.7-release/JBrowse-1.16.7-desktop-linux-x64.zip> - JBrowse-1.16.7-desktop-darwin-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.16.7-release/JBrowse-1.16.7-desktop-darwin-x64.zip> Blog post http://jbrowse.org/blog/2020/01/24/jbrowse-1-16-7.html PS: the JBrowse team had a really great time presenting our new work on JBrowse 2 at PSB 2020 and PAG 2020 recently and meeting everyone. Look forward to new announcements about JBrowse 2 in the upcoming months! Minor improvements - Add name regularization for refseqs named MtDNA (issue #1408 <https://github.com/gmod/jbrowse/pull/1408>, @scottcain <https://github.com/scottcain>, @cmdcolin <https://github.com/cmdcolin>) - Improved performance of startup time with large tracklists (issue #1412 <https://github.com/gmod/jbrowse/pull/1412>, @cmdcolin <https://github.com/cmdcolin>) - Improve consistency of scrolling behavior across browsers using normalize-wheel npm package (@cmdcolin <https://github.com/cmdcolin>, @scottcain <https://github.com/scottcain>, issue #1429 <https://github.com/gmod/jbrowse/pull/1429>) - Add trackMetadata->sortFacets boolean flag which can be set to false to disable sorting the facet categories in the left hand column of the faceted track selector. Thanks to Val Wood for championing this issue for pombase! ( @cmdcolin <https://github.com/cmdcolin>) - Add relativeUrl to trackMetadata config so that URLs relative to the data directory can be specified (the standard url config is relative to the jbrowse root). Thanks to @loraine-gueguen <https://github.com/loraine-gueguen> for the report (issue #1457 <https://github.com/gmod/jbrowse/issues/1457>) <http://jbrowse.org/blog/2020/01/24/jbrowse-1-16-7.html#bug-fixes>Bug fixes - Fix bug that has existed since 1.16.0 (since the introduction of @gmod <https://github.com/gmod>/bam) that caused some BAM tags to be missed in feature details under some conditions. - Added a fix for a performance regularization for large tracklists that contain a lot of data. Thanks to @scottcain <https://github.com/scottcain> for reporting (#issue #1412 <https://github.com/gmod/jbrowse/pull/1412>, @cmdcolin <https://github.com/cmdcolin>) - Fixed ability to access remote data directories in desktop app (issue #1413 <https://github.com/gmod/jbrowse/issues/1413>) - Fixed ability to open FASTA files with the .fasta extension in the desktop app. Thanks to @iankorf <https://github.com/iankorf> for reporting (issue #1415 <https://github.com/gmod/jbrowse/issues/1415>, issue #1426 <https://github.com/gmod/jbrowse/pull/1426>, @cmdcolin <https://github.com/cmdcolin>) - Fixed generate-names.pl to not overwrite the name store class (@Bjoernsen <https://github.com/Bjoernsen>, issue #1297 <https://github.com/gmod/jbrowse/issues/1297>, issue #1423 <https://github.com/gmod/jbrowse/pull/1423>) - Fixed some documentation for Content-Range CORs headers and renderAlignment configs (@cmdcolin <https://github.com/cmdcolin>) - Fixed rendering of CRAM hard clipping, which would display mismatches incorrectly (@cmdcolin <https://github.com/cmdcolin>, issue #1440 <https://github.com/gmod/jbrowse/pull/1440>, issue #1438 <https://github.com/gmod/jbrowse/issues/1438>) - Fixed issue where some BAM features were given the incorrect feature ID across blocks (@cmdcolin <https://github.com/cmdcolin>, https://github.com/GMOD/bam-js/pull/36) - Removed monkey patching from the dropdown refseq box, thanks to @lukaw3d <https://github.com/lukaw3d> for finding and fixing (@lukaw3d <https://github.com/lukaw3d>, issue #1439 <https://github.com/gmod/jbrowse/pull/1439>) - Added fix for bigbed files with large headers, e.g. large autoSql schema (@cmdcolin <https://github.com/cmdcolin>) - Make VCF based features have distinct file IDs for similar overlapping features with same ID, ALT, REF, etc. Thanks @scottcain <https://github.com/scottcain> for the report (@cmdcolin <https://github.com/cmdcolin>) |
|
From: Scott C. <sc...@sc...> - 2020-01-21 18:20:39
|
Hi Cristian, You can't use file:/// to open JBrowse, as browsers won't properly execute the JavaScript--it needs to be run through a web browser. You can install apache on a Windows machine, though I haven't done it in a long time, so I'm not the best person for giving advice on it. Are you planning on serving this out to anybody else? If not, you might want to consider looking into the desktop app instead. Scott On Tue, Jan 21, 2020 at 10:05 AM Cristian DIAZ MUNOZ < Cri...@vu...> wrote: > Dear, > > First of all, I'm not sure if this is the proper place to report this kind > of issue, but if it's not, please I would appreciate if I can be redirected > to a more suitable place for this. > > After running setup.sh, all missing prerequisites were installed and both > tests were executed without any error that I could see in the .log file. > However, when I tried to access to the volvox/yeast html link (and if I run > the index.html located in the JBrowser directory) the following error > occurs: > > RequestError: Unable to load > file:///home/path/to/JBrowse/JBrowse-1.16.6/jbrowse.conf?v=0.481632063767109 > status: 0. > > I have to say that I didn't install JBrowse in the ultra-recommended > directory, as I can't find /var/www/html or even /var/www/ on my PC. > > Thank you in advance! > > [image: Logo VUB] <http://www.vub.ac.be/> > > > > > > MSc. Cristian DÍAZ MUÑOZ > > Research Group of Industrial Microbiology and Food Biotechnology > > Department of Bioengineering Sciences > > Faculty of Sciences and Bioengineering Sciences > > Vrije Universiteit Brussel > > VUB – IMDO – Pleinlaan 2 – 1050 Brussels - Belgium > > *T* +32 (0)2 629 32 45 > > *E* cri...@vu... > > www.vub.ac.be - imdo.vub.ac.be - disclaimer > <http://huisstijl.vub.ac.be/styleguide/disclaimer> > > > > [image: http://www.vub.ac.be/sites/vub/files/Handtekening/triangle.png] > > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Cristian D. M. <Cri...@vu...> - 2020-01-21 18:05:34
|
Dear, First of all, I'm not sure if this is the proper place to report this kind of issue, but if it's not, please I would appreciate if I can be redirected to a more suitable place for this. After running setup.sh, all missing prerequisites were installed and both tests were executed without any error that I could see in the .log file. However, when I tried to access to the volvox/yeast html link (and if I run the index.html located in the JBrowser directory) the following error occurs: RequestError: Unable to load file:///home/path/to/JBrowse/JBrowse-1.16.6/jbrowse.conf?v=0.481632063767109 status: 0. I have to say that I didn't install JBrowse in the ultra-recommended directory, as I can't find /var/www/html or even /var/www/ on my PC. Thank you in advance! [Logo VUB]<http://www.vub.ac.be/> MSc. Cristian DÍAZ MUÑOZ Research Group of Industrial Microbiology and Food Biotechnology Department of Bioengineering Sciences Faculty of Sciences and Bioengineering Sciences Vrije Universiteit Brussel VUB – IMDO – Pleinlaan 2 – 1050 Brussels - Belgium T +32 (0)2 629 32 45 E cri...@vu... www.vub.ac.be<http://www.vub.ac.be/> - imdo.vub.ac.be<http://imdo.vub.ac.be/> - disclaimer<http://huisstijl.vub.ac.be/styleguide/disclaimer> [http://www.vub.ac.be/sites/vub/files/Handtekening/triangle.png] |
|
From: Scott C. <sc...@sc...> - 2020-01-21 18:01:25
|
Actually, depending what the changes look like (that is, if I could be confident that one change wouldn't be mistaken for another), I might write a much simpler script that used a table of changes and a simple regex that operated over the whole GFF file per change. It might take a while to run depending on how big the file is and how many changes there are to make, but it would be easy to write. On Tue, Jan 21, 2020 at 9:53 AM Scott Cain <sc...@sc...> wrote: > Probably but I feel like it would be more complicated. > > On Mon, Jan 20, 2020 at 5:16 PM Fields, Christopher J < > cjf...@il...> wrote: > >> I vaguely recall doing something like this a few years ago w/ >> Bio::FeatureIO but it was custom. Would this be possible in >> Bio::DB::SeqFeature? >> >> >> >> chris >> >> >> >> *From: *Scott Cain <sc...@sc...> >> *Date: *Monday, January 20, 2020 at 6:52 PM >> *To: *"Michał T. Lorenc" <m.t...@gm...> >> *Cc: *gmod-ajax <gmo...@li...> >> *Subject: *Re: [Gmod-ajax] changing ID in an existing GFF3 file >> >> >> >> Hi Michal, >> >> >> >> I don't know of any general purpose script for doing that. If I were >> writing one, I'd probably do it with a perl script that used >> Bio::FeatureIO::gff, but then, I'm old :-) >> >> >> >> Sorry I couldn't be more helpful, >> >> Scott >> >> >> >> >> >> On Sun, Jan 19, 2020 at 1:59 PM Michał T. Lorenc <m.t...@gm...> >> wrote: >> >> Hi all, >> I ran BRAKER2 annotation pipeline and now I would like to change the ids >> from e.g. g65212 to AT1G01010.1, AT1G01020.1, AT1G01030.1.... Is there a >> script available to change IDs in an existing GFF3 file? >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> *NbV1Ch01 TAIR10 gene 5928 8737 . - . >> ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020 NbV1Ch01 TAIR10 >> mRNA 5928 8737 . - . >> ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1 NbV1Ch01 >> TAIR10 protein 6915 8666 . - . >> ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1 >> NbV1Ch01 TAIR10 five_prime_UTR 8667 8737 . - . >> Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 8571 8666 . >> - 0 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 8571 >> 8737 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 >> CDS 8417 8464 . - 0 Parent=AT1G01020.1 >> NbV1Ch01 TAIR10 exon 8417 8464 . - . >> Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 8236 8325 . >> - 0 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 8236 >> 8325 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 >> CDS 7942 7987 . - 0 Parent=AT1G01020.1 >> NbV1Ch01 TAIR10 exon 7942 7987 . - . >> Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 7762 7835 . >> - 2 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 7762 >> 7835 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 >> CDS 7564 7649 . - 0 Parent=AT1G01020.1 >> NbV1Ch01 TAIR10 exon 7564 7649 . - . >> Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 7384 7450 . >> - 1 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 7384 >> 7450 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 >> CDS 7157 7232 . - 0 Parent=AT1G01020.1 >> NbV1Ch01 TAIR10 exon 7157 7232 . - . >> Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 6915 7069 . >> - 2 Parent=AT1G01020.1 NbV1Ch01 TAIR10 three_prime_UTR >> 6437 6914 . - . Parent=AT1G01020.1 NbV1Ch01 >> TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1 >> NbV1Ch01 TAIR10 three_prime_UTR 5928 6263 . - . >> Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 5928 6263 . >> - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 mRNA 6790 >> 8737 . - . >> ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;Index=1 NbV1Ch01 >> TAIR10 protein 7315 8666 . - . >> ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2 >> NbV1Ch01 TAIR10 five_prime_UTR 8667 8737 . - . >> Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 8571 8666 . >> - 0 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 8571 >> 8737 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10 >> CDS 8417 8464 . - 0 Parent=AT1G01020.2 >> NbV1Ch01 TAIR10 exon 8417 8464 . - . >> Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 8236 8325 . >> - 0 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 8236 >> 8325 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10 >> CDS 7942 7987 . - 0 Parent=AT1G01020.2 >> NbV1Ch01 TAIR10 exon 7942 7987 . - . >> Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 7762 7835 . >> - 2 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 7762 >> 7835 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10 >> CDS 7564 7649 . - 0 Parent=AT1G01020.2 >> NbV1Ch01 TAIR10 exon 7564 7649 . - . >> Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 7315 7450 . >> - 1 Parent=AT1G01020.2 NbV1Ch01 TAIR10 three_prime_UTR >> 7157 7314 . - . Parent=AT1G01020.2 NbV1Ch01 >> TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2 >> NbV1Ch01 TAIR10 three_prime_UTR 6790 7069 . - . >> Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 6790 7069 . >> - . Parent=AT1G01020.2* >> >> Thank you in advance, >> >> Michal >> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> >> >> >> -- >> >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Scott C. <sc...@sc...> - 2020-01-21 17:54:11
|
Probably but I feel like it would be more complicated. On Mon, Jan 20, 2020 at 5:16 PM Fields, Christopher J <cjf...@il...> wrote: > I vaguely recall doing something like this a few years ago w/ > Bio::FeatureIO but it was custom. Would this be possible in > Bio::DB::SeqFeature? > > > > chris > > > > *From: *Scott Cain <sc...@sc...> > *Date: *Monday, January 20, 2020 at 6:52 PM > *To: *"Michał T. Lorenc" <m.t...@gm...> > *Cc: *gmod-ajax <gmo...@li...> > *Subject: *Re: [Gmod-ajax] changing ID in an existing GFF3 file > > > > Hi Michal, > > > > I don't know of any general purpose script for doing that. If I were > writing one, I'd probably do it with a perl script that used > Bio::FeatureIO::gff, but then, I'm old :-) > > > > Sorry I couldn't be more helpful, > > Scott > > > > > > On Sun, Jan 19, 2020 at 1:59 PM Michał T. Lorenc <m.t...@gm...> > wrote: > > Hi all, > I ran BRAKER2 annotation pipeline and now I would like to change the ids > from e.g. g65212 to AT1G01010.1, AT1G01020.1, AT1G01030.1.... Is there a > script available to change IDs in an existing GFF3 file? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *NbV1Ch01 TAIR10 gene 5928 8737 . - . > ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020 NbV1Ch01 TAIR10 > mRNA 5928 8737 . - . > ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1 NbV1Ch01 > TAIR10 protein 6915 8666 . - . > ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1 > NbV1Ch01 TAIR10 five_prime_UTR 8667 8737 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 8571 8666 . > - 0 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 8571 > 8737 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 > CDS 8417 8464 . - 0 Parent=AT1G01020.1 > NbV1Ch01 TAIR10 exon 8417 8464 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 8236 8325 . > - 0 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 8236 > 8325 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 > CDS 7942 7987 . - 0 Parent=AT1G01020.1 > NbV1Ch01 TAIR10 exon 7942 7987 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 7762 7835 . > - 2 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 7762 > 7835 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 > CDS 7564 7649 . - 0 Parent=AT1G01020.1 > NbV1Ch01 TAIR10 exon 7564 7649 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 7384 7450 . > - 1 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 7384 > 7450 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 > CDS 7157 7232 . - 0 Parent=AT1G01020.1 > NbV1Ch01 TAIR10 exon 7157 7232 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 6915 7069 . > - 2 Parent=AT1G01020.1 NbV1Ch01 TAIR10 three_prime_UTR > 6437 6914 . - . Parent=AT1G01020.1 NbV1Ch01 > TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1 > NbV1Ch01 TAIR10 three_prime_UTR 5928 6263 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 5928 6263 . > - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 mRNA 6790 > 8737 . - . > ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;Index=1 NbV1Ch01 > TAIR10 protein 7315 8666 . - . > ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2 > NbV1Ch01 TAIR10 five_prime_UTR 8667 8737 . - . > Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 8571 8666 . > - 0 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 8571 > 8737 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10 > CDS 8417 8464 . - 0 Parent=AT1G01020.2 > NbV1Ch01 TAIR10 exon 8417 8464 . - . > Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 8236 8325 . > - 0 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 8236 > 8325 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10 > CDS 7942 7987 . - 0 Parent=AT1G01020.2 > NbV1Ch01 TAIR10 exon 7942 7987 . - . > Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 7762 7835 . > - 2 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 7762 > 7835 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10 > CDS 7564 7649 . - 0 Parent=AT1G01020.2 > NbV1Ch01 TAIR10 exon 7564 7649 . - . > Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 7315 7450 . > - 1 Parent=AT1G01020.2 NbV1Ch01 TAIR10 three_prime_UTR > 7157 7314 . - . Parent=AT1G01020.2 NbV1Ch01 > TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2 > NbV1Ch01 TAIR10 three_prime_UTR 6790 7069 . - . > Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 6790 7069 . > - . Parent=AT1G01020.2* > > Thank you in advance, > > Michal > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > > -- > > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Fields, C. J <cjf...@il...> - 2020-01-21 01:16:42
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I vaguely recall doing something like this a few years ago w/ Bio::FeatureIO but it was custom. Would this be possible in Bio::DB::SeqFeature?
chris
From: Scott Cain <sc...@sc...>
Date: Monday, January 20, 2020 at 6:52 PM
To: "Michał T. Lorenc" <m.t...@gm...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] changing ID in an existing GFF3 file
Hi Michal,
I don't know of any general purpose script for doing that. If I were writing one, I'd probably do it with a perl script that used Bio::FeatureIO::gff, but then, I'm old :-)
Sorry I couldn't be more helpful,
Scott
On Sun, Jan 19, 2020 at 1:59 PM Michał T. Lorenc <m.t...@gm...<mailto:m.t...@gm...>> wrote:
Hi all,
I ran BRAKER2 annotation pipeline and now I would like to change the ids from e.g. g65212 to AT1G01010.1, AT1G01020.1, AT1G01030.1.... Is there a script available to change IDs in an existing GFF3 file?
NbV1Ch01 TAIR10 gene 5928 8737 . - . ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020
NbV1Ch01 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1
NbV1Ch01 TAIR10 protein 6915 8666 . - . ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1
NbV1Ch01 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 CDS 8571 8666 . - 0 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 CDS 8417 8464 . - 0 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 CDS 8236 8325 . - 0 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 CDS 7942 7987 . - 0 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 CDS 7762 7835 . - 2 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 CDS 7564 7649 . - 0 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 CDS 7384 7450 . - 1 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 7384 7450 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 CDS 7157 7232 . - 0 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 7157 7232 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 CDS 6915 7069 . - 2 Parent=AT1G01020.1
NbV1Ch01 TAIR10 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 5928 6263 . - . Parent=AT1G01020.1
NbV1Ch01 TAIR10 mRNA 6790 8737 . - . ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;Index=1
NbV1Ch01 TAIR10 protein 7315 8666 . - . ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2
NbV1Ch01 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2
NbV1Ch01 TAIR10 CDS 8571 8666 . - 0 Parent=AT1G01020.2
NbV1Ch01 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.2
NbV1Ch01 TAIR10 CDS 8417 8464 . - 0 Parent=AT1G01020.2
NbV1Ch01 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.2
NbV1Ch01 TAIR10 CDS 8236 8325 . - 0 Parent=AT1G01020.2
NbV1Ch01 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.2
NbV1Ch01 TAIR10 CDS 7942 7987 . - 0 Parent=AT1G01020.2
NbV1Ch01 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.2
NbV1Ch01 TAIR10 CDS 7762 7835 . - 2 Parent=AT1G01020.2
NbV1Ch01 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.2
NbV1Ch01 TAIR10 CDS 7564 7649 . - 0 Parent=AT1G01020.2
NbV1Ch01 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.2
NbV1Ch01 TAIR10 CDS 7315 7450 . - 1 Parent=AT1G01020.2
NbV1Ch01 TAIR10 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2
NbV1Ch01 TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2
NbV1Ch01 TAIR10 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2
NbV1Ch01 TAIR10 exon 6790 7069 . - . Parent=AT1G01020.2
Thank you in advance,
Michal
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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From: Scott C. <sc...@sc...> - 2020-01-21 00:52:09
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Hi Michal, I don't know of any general purpose script for doing that. If I were writing one, I'd probably do it with a perl script that used Bio::FeatureIO::gff, but then, I'm old :-) Sorry I couldn't be more helpful, Scott On Sun, Jan 19, 2020 at 1:59 PM Michał T. Lorenc <m.t...@gm...> wrote: > Hi all, > I ran BRAKER2 annotation pipeline and now I would like to change the ids > from e.g. g65212 to AT1G01010.1, AT1G01020.1, AT1G01030.1.... Is there a > script available to change IDs in an existing GFF3 file? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *NbV1Ch01 TAIR10 gene 5928 8737 . - . > ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020 NbV1Ch01 TAIR10 > mRNA 5928 8737 . - . > ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1 NbV1Ch01 > TAIR10 protein 6915 8666 . - . > ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1 > NbV1Ch01 TAIR10 five_prime_UTR 8667 8737 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 8571 8666 . - > 0 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 8571 > 8737 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 > CDS 8417 8464 . - 0 Parent=AT1G01020.1 > NbV1Ch01 TAIR10 exon 8417 8464 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 8236 8325 . - > 0 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 8236 > 8325 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 > CDS 7942 7987 . - 0 Parent=AT1G01020.1 > NbV1Ch01 TAIR10 exon 7942 7987 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 7762 7835 . - > 2 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 7762 > 7835 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 > CDS 7564 7649 . - 0 Parent=AT1G01020.1 > NbV1Ch01 TAIR10 exon 7564 7649 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 7384 7450 . - > 1 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 7384 > 7450 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 > CDS 7157 7232 . - 0 Parent=AT1G01020.1 > NbV1Ch01 TAIR10 exon 7157 7232 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 6915 7069 . - > 2 Parent=AT1G01020.1 NbV1Ch01 TAIR10 three_prime_UTR > 6437 6914 . - . Parent=AT1G01020.1 NbV1Ch01 > TAIR10 exon 6437 7069 . - . > Parent=AT1G01020.1 NbV1Ch01 TAIR10 three_prime_UTR 5928 6263 . > - . Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon > 5928 6263 . - . Parent=AT1G01020.1 NbV1Ch01 > TAIR10 mRNA 6790 8737 . - . > ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;Index=1 NbV1Ch01 > TAIR10 protein 7315 8666 . - . > ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2 > NbV1Ch01 TAIR10 five_prime_UTR 8667 8737 . - . > Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 8571 8666 . - > 0 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 8571 > 8737 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10 > CDS 8417 8464 . - 0 Parent=AT1G01020.2 > NbV1Ch01 TAIR10 exon 8417 8464 . - . > Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 8236 8325 . - > 0 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 8236 > 8325 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10 > CDS 7942 7987 . - 0 Parent=AT1G01020.2 > NbV1Ch01 TAIR10 exon 7942 7987 . - . > Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 7762 7835 . - > 2 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 7762 > 7835 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10 > CDS 7564 7649 . - 0 Parent=AT1G01020.2 > NbV1Ch01 TAIR10 exon 7564 7649 . - . > Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 7315 7450 . - > 1 Parent=AT1G01020.2 NbV1Ch01 TAIR10 three_prime_UTR > 7157 7314 . - . Parent=AT1G01020.2 NbV1Ch01 > TAIR10 exon 7157 7450 . - . > Parent=AT1G01020.2 NbV1Ch01 TAIR10 three_prime_UTR 6790 7069 . > - . Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon > 6790 7069 . - . Parent=AT1G01020.2* > > Thank you in advance, > > Michal > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Michał T. L. <m.t...@gm...> - 2020-01-19 21:59:48
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Hi all,
I ran BRAKER2 annotation pipeline and now I would like to change the ids
from e.g. g65212 to AT1G01010.1, AT1G01020.1, AT1G01030.1.... Is there a
script available to change IDs in an existing GFF3 file?
*NbV1Ch01 TAIR10 gene 5928 8737 . - .
ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020 NbV1Ch01 TAIR10
mRNA 5928 8737 . - .
ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1 NbV1Ch01
TAIR10 protein 6915 8666 . - .
ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1
NbV1Ch01 TAIR10 five_prime_UTR 8667 8737 . - .
Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 8571 8666 . -
0 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 8571
8737 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10
CDS 8417 8464 . - 0 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 8417 8464 . - .
Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 8236 8325 . -
0 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 8236
8325 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10
CDS 7942 7987 . - 0 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 7942 7987 . - .
Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 7762 7835 . -
2 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 7762
7835 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10
CDS 7564 7649 . - 0 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 7564 7649 . - .
Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 7384 7450 . -
1 Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon 7384
7450 . - . Parent=AT1G01020.1 NbV1Ch01 TAIR10
CDS 7157 7232 . - 0 Parent=AT1G01020.1
NbV1Ch01 TAIR10 exon 7157 7232 . - .
Parent=AT1G01020.1 NbV1Ch01 TAIR10 CDS 6915 7069 . -
2 Parent=AT1G01020.1 NbV1Ch01 TAIR10 three_prime_UTR
6437 6914 . - . Parent=AT1G01020.1 NbV1Ch01
TAIR10 exon 6437 7069 . - .
Parent=AT1G01020.1 NbV1Ch01 TAIR10 three_prime_UTR 5928 6263 .
- . Parent=AT1G01020.1 NbV1Ch01 TAIR10 exon
5928 6263 . - . Parent=AT1G01020.1 NbV1Ch01
TAIR10 mRNA 6790 8737 . - .
ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;Index=1 NbV1Ch01
TAIR10 protein 7315 8666 . - .
ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2
NbV1Ch01 TAIR10 five_prime_UTR 8667 8737 . - .
Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 8571 8666 . -
0 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 8571
8737 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10
CDS 8417 8464 . - 0 Parent=AT1G01020.2
NbV1Ch01 TAIR10 exon 8417 8464 . - .
Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 8236 8325 . -
0 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 8236
8325 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10
CDS 7942 7987 . - 0 Parent=AT1G01020.2
NbV1Ch01 TAIR10 exon 7942 7987 . - .
Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 7762 7835 . -
2 Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon 7762
7835 . - . Parent=AT1G01020.2 NbV1Ch01 TAIR10
CDS 7564 7649 . - 0 Parent=AT1G01020.2
NbV1Ch01 TAIR10 exon 7564 7649 . - .
Parent=AT1G01020.2 NbV1Ch01 TAIR10 CDS 7315 7450 . -
1 Parent=AT1G01020.2 NbV1Ch01 TAIR10 three_prime_UTR
7157 7314 . - . Parent=AT1G01020.2 NbV1Ch01
TAIR10 exon 7157 7450 . - .
Parent=AT1G01020.2 NbV1Ch01 TAIR10 three_prime_UTR 6790 7069 .
- . Parent=AT1G01020.2 NbV1Ch01 TAIR10 exon
6790 7069 . - . Parent=AT1G01020.2*
Thank you in advance,
Michal
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From: Nathan D. <nat...@lb...> - 2019-12-19 20:48:13
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> Begin forwarded message: > > From: Dave Clements <cle...@gm...> > Subject: [GMOD-devel] BCC2020 and Galaxy Admin Training > Date: December 19, 2019 at 12:06:31 PM PST > To: Galaxy Announcements List <gal...@li...>, Galaxy Dev List <gal...@li...>, GMOD Announcements List <gmo...@li...>, GMOD Developers List <gmo...@li...>, BCC2020 Organizers <bcc...@li...> > > Hello all, > > There are three things going on that are of general interest to the Galaxy and GMOD communities, and that have some urgency to them (and thus this mid-month email). > > BCC2020 Schedule Structure > ----------------------- > The Bioinformatics Community Conference (BCC2020, https://bcc2020.github.io/ <https://bcc2020.github.io/>) will be held in July, in Toronto, right after ISMB in Montréal. This event brings together the BOSC and Galaxy communities into one gathering. > > If you are considering attending BCC2020, then the organizers would like your input on several scheduling choices, BY JANUARY 7: > https://bcc2020.github.io/blog/poll <https://bcc2020.github.io/blog/poll> > > BCC2020 Training Topic Nominations > ------------------------ > The training offered at BCC2020 is determined by the community. We are now accepting nominations for training sessions. Nominated topics will be voted on by the community. Please submit your ideas by JANUARY 17. > https://bcc2020.github.io/blog/training-nom <https://bcc2020.github.io/blog/training-nom> > > 2020 Galaxy Admin Training > ----------------------- > A week long workshop on setting up your own production-grade Galaxy instance will be held in Barcelona the first week of March. Registration is now open, and is, well, pretty darn cheap too. > https://galaxyproject.org/events/2020-03-admin/ <https://galaxyproject.org/events/2020-03-admin/> > > > And, of course, there is a lot of other stuff going on too: > https://galaxyproject.org/events/ <https://galaxyproject.org/events/> > > Happy Holidays, and hope to see you in the new year! > > Dave C, on behalf of the BCC2020 and Galaxy Admin Training organizers > > -- > https://galaxyproject.org/ <https://galaxyproject.org/> > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel |
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From: Nathan D. <nat...@lb...> - 2019-11-27 19:24:32
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Apollo 2.5.0 has been released: https://github.com/GMOD/Apollo/releases/tag/2.5.0 <https://github.com/GMOD/Apollo/releases/tag/2.5.0> Major features include: Moved blat / blast search to its own tab Allow creation of annotations from blat features On upload of fasta file execute faToTwoBit if present to create searchable blat file Allows history tracking for non-structural edits There are numerous bug fixes and web-service fixes. More changes can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md <https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md> Docker builds are on quay.io and docker hub: https://quay.io/repository/gmod/apollo?tab=builds <https://quay.io/repository/gmod/apollo?tab=builds> https://hub.docker.com/r/gmod/apollo <https://hub.docker.com/r/gmod/apollo> Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/ <http://genomearchitect.readthedocs.io/en/latest/> Note: You can find a guide upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html <https://genomearchitect.readthedocs.io/en/latest/Migration.html> Report issues if found on GitHub https://github.com/GMOD/Apollo/issues <https://github.com/GMOD/Apollo/issues> General issues questions / comments should go to the mailing list (ap...@lb... <mailto:ap...@lb...>) on google groups (https://groups.google.com/a/lbl.gov/forum/#!forum/apollo <https://groups.google.com/a/lbl.gov/forum/#!forum/apollo>). AWS EC2 Community images of Apollo 2.5.0 will be available within the N. Virginia and California regions minimally. Please request on the forum or ticketing system if more are needed. Cheers! Apollo developers |
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From: Scott C. <sc...@sc...> - 2019-11-19 03:35:50
|
Hello, As announced last month, there will be a GMOD codefest held before the Plant and Animal Genome meeting in San Diego, January 9-10, 2020. The meeting will be held at the Handlery hotel (down the street from the Town and Country Hotel). Logistical and other information can be found at the GMOD wiki as the details become more solid: http://gmod.org/wiki/Codefest_2020 Several potential projects are described in this document: https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit We know for sure that there will be developers from the Tripal, Apollo, JBrowse, and Chado projects. Of course, other projects like Galaxy, InterMine, and MAKER are welcome too! See you in San Diego! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Nathan D. <nat...@lb...> - 2019-11-05 21:01:16
|
Just to follow-up, more details can be found here. https://github.com/GMOD/Apollo/issues/2190#issuecomment-515651504 On Saturday, July 27, 2019 at 5:11:06 PM UTC-7, Michał T. Lorenc wrote: > > Hi, > I tried to install ElasticSearch plugin ( > https://github.com/elsiklab/jbrowse_elasticsearch ) into Apollo. With the > following steps: > > > 1. git clone https://github.com/GMOD/Apollo.git > 2. cd Apollo > 3. I added ElasticSearch to `cat > docker-files/docker-apollo-config.groovy` > > > > > > > > > > > > > > > > > > *```jbrowse { git { url = "https://github.com/GMOD/jbrowse > <https://github.com/GMOD/jbrowse>" branch = "1.16.4-release" } > plugins { ... ElasticSearch{ git = > 'https://github.com/elsiklab/jbrowse_elasticsearch > <https://github.com/elsiklab/jbrowse_elasticsearch>' branch = > 'master' alwaysRecheck = "true" alwaysPull = > "true" } }}* > ``` > Next, I executed > > > > > *```docker build -t apollo .docker run -it -v "$(pwd)"/mydata:/data -p > 8888:8080 -p 8080:3000 apollo```* > > - http://localhost:8080/ does not work for elasticsearch > - http://localhost:8888/ only Apollo works without elasticsearch > > What did I miss? > > Thank you in advance, > > Michal > > > > > |
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From: Victor de J. <vic...@gm...> - 2019-10-24 13:05:54
|
Hi Colin, it works now. I had a space in the tracklist which skips the last track, given generate-names.pl -mem 4096000000 -out /data/apollo/ourgenome/data --tracks "ourgenome.gff3.gz", "ourgenome.markers.vcf.gz" --verbose generate-names.pl -mem 4096000000 -out /data/apollo/ourgenome/data --tracks "ourgenome.gff3.gz","ourgenome.markers.vcf.gz" --verbose ^ Victor On Thu, Oct 24, 2019 at 2:19 PM Colin <col...@gm...> wrote: > The generate-names.pl script will index IDs from the VCF and should just > do this by default > > Our demo browser has this for example > > > http://jbrowse.org/code/JBrowse-1.16.6/?data=sample_data/json/volvox&loc=rs114905802 > > It doesn't have any tools for indexing from the INFO column but this is an > enhancement that could be added (GFF3 tabix was recently updated to from > the column9 for example) > > If it's not working maybe we may need more info on the setup > > -Colin > > On Thu, Oct 24, 2019 at 6:22 AM Victor de Jager <vic...@gm...> > wrote: > >> Hi all, >> >> I'm using a VCF track to show markers in jbrowse. would it be possible to >> index the ID column or one of the INFO attributes, just like the ID and >> Name attributes from a GFF3 track? >> >> Best regards, >> >> Victor >> >> >> >> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
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From: Colin <col...@gm...> - 2019-10-24 12:19:53
|
The generate-names.pl script will index IDs from the VCF and should just do this by default Our demo browser has this for example http://jbrowse.org/code/JBrowse-1.16.6/?data=sample_data/json/volvox&loc=rs114905802 It doesn't have any tools for indexing from the INFO column but this is an enhancement that could be added (GFF3 tabix was recently updated to from the column9 for example) If it's not working maybe we may need more info on the setup -Colin On Thu, Oct 24, 2019 at 6:22 AM Victor de Jager <vic...@gm...> wrote: > Hi all, > > I'm using a VCF track to show markers in jbrowse. would it be possible to > index the ID column or one of the INFO attributes, just like the ID and > Name attributes from a GFF3 track? > > Best regards, > > Victor > > > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Victor de J. <vic...@gm...> - 2019-10-24 09:29:15
|
Hi all, I'm using a VCF track to show markers in jbrowse. would it be possible to index the ID column or one of the INFO attributes, just like the ID and Name attributes from a GFF3 track? Best regards, Victor |
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From: Nathan D. <nat...@lb...> - 2019-10-10 23:01:31
|
I plan on being there to work on user’s Apollo-based problems (or JBrowse ones if that is more pertinent). I’ve copied on the Apollo list. Looking forward to seeing you there, Nathan > On Oct 10, 2019, at 2:40 PM, Scott Cain <sc...@sc...> wrote: > > I am pleased to announce there will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc <https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>, JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy <http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>. We already know that there will be Tripal, Chado and JBrowse developers present. Registration information will be coming soon. > > You can follow the changes to this page: > > http://gmod.org/wiki/Codefest_2020 <http://gmod.org/wiki/Codefest_2020> > > to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter. > > See you in San Diego, > Scott > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/ <http://gmod.org/>) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel |
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From: Scott C. <sc...@sc...> - 2019-10-10 21:40:50
|
I am pleased to announce there will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc <https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>, JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy <http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>. We already know that there will be Tripal, Chado and JBrowse developers present. Registration information will be coming soon. You can follow the changes to this page: http://gmod.org/wiki/Codefest_2020 to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter. See you in San Diego, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Scott C. <sc...@sc...> - 2019-09-20 16:36:41
|
Hi Qingdong, If you are a JBrowse admin, you can add refSeqSelectorMaxSize = 45 to your jbrowse.conf file, as described here: https://jbrowse.org/docs/reference_sequence.html If you don't administer the JBrowse site you're referring to, you'll have to contact the owner and ask them to do this. In this case, you can also put the name of the "missing" chromosomes in the search box to get them (which I realize is not ideal, but at least the data are there). Scott On Fri, Sep 20, 2019 at 9:31 AM z qd <zqd...@ho...> wrote: > Dear, > When I use jbrowse to view my data, the chromosome number is 45, while the > jbrowse only show the first 30 red seqs, how can I fix the problem? > > Best wishes, > Qingdong > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: z qd <zqd...@ho...> - 2019-09-20 02:07:52
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Dear, When I use jbrowse to view my data, the chromosome number is 45, while the jbrowse only show the first 30 red seqs, how can I fix the problem? Best wishes, Qingdong |
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From: Colin <col...@gm...> - 2019-09-10 15:48:25
|
There is a maxHeight configuration variable that you can change to a high number -Colin On Tue, Sep 10, 2019 at 8:34 AM Michał T. Lorenc <m.t...@gm...> wrote: > Hi all, > After HiSAT2 I ran MarkDuplicates and removed aligned reads with lower > than 40 quaily score but still, I get Max height reached. > > [image: Screen Shot 2019-09-11 at 12.23.00 AM.png] > > Is there a way to change the aligned reads so there do not trigger Max > height reached and covering the whole gene region? > > Thank you in advance > > Michal > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Michał T. L. <m.t...@gm...> - 2019-09-10 14:34:20
|
Hi all, After HiSAT2 I ran MarkDuplicates and removed aligned reads with lower than 40 quaily score but still, I get Max height reached. [image: Screen Shot 2019-09-11 at 12.23.00 AM.png] Is there a way to change the aligned reads so there do not trigger Max height reached and covering the whole gene region? Thank you in advance Michal |
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From: Colin <col...@gm...> - 2019-08-29 22:28:27
|
I don't think I use the outfmt 6 command with the blastn/tblastn command
-Colin
On Thu, Aug 29, 2019 at 6:25 PM Michał T. Lorenc <m.t...@gm...>
wrote:
> Hi Colin,
> I tried your command but the output file is empty
>
> > bp_search2gff.pl --input all-tblastn.1000.out --addid --version 3
> --type hit
> or
> > bp_search2gff.pl --input all-tblastn.1000.out --output all-tblastn.gff3
> --addid --version 3 --type hit
>
> > tblastn -query $fa -db $3 -num_threads 4 -outfmt 6 > ${4}/${input}_${db}
>
> What did I miss?
>
> Thank you in advance,
>
> Michal
>
>
> On Fri, Aug 30, 2019 at 2:54 AM Colin <col...@gm...> wrote:
>
>> My usage of the bp_search2gff command has been like this
>>
>> https://www.biostars.org/p/277/#171458
>>
>>
>> Query step
>>
>> blastn -query query.fa -db blast.fa > blast.txt
>>
>> Run bp_search2gff.pl
>>
>> bp_search2gff.pl --input blast.txt --addid --version 3 --type hit
>>
>> -Colin
>>
>>
>> On Thu, Aug 29, 2019 at 10:46 AM Michał T. Lorenc <m.t...@gm...>
>> wrote:
>>
>>> Hi all,
>>> I ran tblastn and have got this Blast output:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *NIATv7_g23718.t1 NbV1Ch10 95.789 95 4 0
>>> 596 690 12945534 12945818 2.55e-49
>>> 193NIATv7_g23718.t1 NbV1Ch10 70.290 138 4 1
>>> 473 573 12943183 12943596 9.76e-46
>>> 182NIATv7_g23718.t1 NbV1Ch10 70.290 138 4 1
>>> 472 572 12943180 12943593 1.36e-44
>>> 179NIATv7_g23718.t1 NbV1Ch10 97.561 41 1 0
>>> 122 162 12937586 12937708 1.02e-29
>>> 85.5NIATv7_g23718.t1 NbV1Ch10 93.939 33 2 0
>>> 91 123 12937413 12937511 1.02e-29
>>> 70.9NIATv7_g23718.t1 NbV1Ch10 91.111 45 4 0
>>> 435 479 12942868 12943002 1.14e-28
>>> 84.7NIATv7_g23718.t1 NbV1Ch10 100.000 31 0 0
>>> 405 435 12942669 12942761 1.14e-28
>>> 67.8NIATv7_g23718.t1 NbV1Ch10 97.500 40 1 0
>>> 171 210 12938519 12938638 4.58e-16
>>> 87.8NIATv7_g23718.t1 NbV1Ch10 81.818 11 2 0
>>> 161 171 12938374 12938406 4.58e-16
>>> 22.3NIATv7_g23718.t1 NbV1Ch10 83.333 48 8 0
>>> 271 318 12939766 12939909 2.79e-15
>>> 86.7NIATv7_g23718.t1 NbV1Ch10 94.737 38 2 0
>>> 33 70 12931492 12931605 2.30e-13
>>> 80.5NIATv7_g23718.t1 NbV1Ch10 82.857 35 6 0
>>> 251 285 12939588 12939692 5.41e-09
>>> 66.2NIATv7_g23718.t1 NbV1Ch10 100.000 31 0 0
>>> 317 347 12940034 12940126 1.12e-08
>>> 65.1NIATv7_g23718.t1 NbV1Ch10 96.970 33 1 0
>>> 1 33 12931031 12931129 1.22e-08
>>> 65.1NIATv7_g23718.t1 NbV1Ch10 75.000 40 10 0
>>> 336 375 12940960 12941079 1.07e-07
>>> 62.0NIATv7_g23718.t1 NbV1Ch10 100.000 29 0 0
>>> 223 251 12938772 12938858 3.82e-07
>>> 60.1NIATv7_g23718.t1 NbV1Ch10 95.652 23 1 0
>>> 70 92 12932440 12932508 0.014
>>> 45.1NIATv7_g23718.t1 NbV1Ch01 80.000 60 12 0
>>> 473 532 135384227 135384048 2.25e-37
>>> 96.3NIATv7_g23718.t1 NbV1Ch01 82.692 52 9 0
>>> 529 580 135383956 135383801 2.25e-37
>>> 85.9NIATv7_g23718.t1 NbV1Ch01 92.683 41 3 0
>>> 122 162 135393270 135393148 1.89e-27
>>> 82.8NIATv7_g23718.t1 NbV1Ch01 90.625 32 3 0
>>> 92 123 135393437 135393342 1.89e-27
>>> 65.5NIATv7_g23718.t1 NbV1Ch01 73.626 91 20 3
>>> 595 682 135374896 135374627 1.62e-22
>>> 110NIATv7_g23718.t1 NbV1Ch01 72.500 40 11 0
>>> 31 70 135399457 135399338 7.51e-21 67.8*
>>>
>>> Next, I ran the below command which is part of BioPerl in order to
>>> generate a gff3 file for Jbrowse:
>>>
>>> *bp_search2gff.pl <http://bp_search2gff.pl> --in all-tblastn.1000.out
>>> --out all-tblastn.gff3 --version 3 -f blast --match --source
>>> tBLASTn.NitVsNb --type hit*
>>>
>>> However, the command has generated an empty file. Did I use command
>>> wrongly or is there another way to add Blast tracks to JBrowse?
>>>
>>> Thank you in advance,
>>>
>>> Michal
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
|
|
From: Michał T. L. <m.t...@gm...> - 2019-08-29 22:25:30
|
Hi Colin,
I tried your command but the output file is empty
> bp_search2gff.pl --input all-tblastn.1000.out --addid --version 3 --type
hit
or
> bp_search2gff.pl --input all-tblastn.1000.out --output all-tblastn.gff3
--addid --version 3 --type hit
> tblastn -query $fa -db $3 -num_threads 4 -outfmt 6 > ${4}/${input}_${db}
What did I miss?
Thank you in advance,
Michal
On Fri, Aug 30, 2019 at 2:54 AM Colin <col...@gm...> wrote:
> My usage of the bp_search2gff command has been like this
>
> https://www.biostars.org/p/277/#171458
>
>
> Query step
>
> blastn -query query.fa -db blast.fa > blast.txt
>
> Run bp_search2gff.pl
>
> bp_search2gff.pl --input blast.txt --addid --version 3 --type hit
>
> -Colin
>
>
> On Thu, Aug 29, 2019 at 10:46 AM Michał T. Lorenc <m.t...@gm...>
> wrote:
>
>> Hi all,
>> I ran tblastn and have got this Blast output:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *NIATv7_g23718.t1 NbV1Ch10 95.789 95 4 0
>> 596 690 12945534 12945818 2.55e-49
>> 193NIATv7_g23718.t1 NbV1Ch10 70.290 138 4 1
>> 473 573 12943183 12943596 9.76e-46
>> 182NIATv7_g23718.t1 NbV1Ch10 70.290 138 4 1
>> 472 572 12943180 12943593 1.36e-44
>> 179NIATv7_g23718.t1 NbV1Ch10 97.561 41 1 0
>> 122 162 12937586 12937708 1.02e-29
>> 85.5NIATv7_g23718.t1 NbV1Ch10 93.939 33 2 0
>> 91 123 12937413 12937511 1.02e-29
>> 70.9NIATv7_g23718.t1 NbV1Ch10 91.111 45 4 0
>> 435 479 12942868 12943002 1.14e-28
>> 84.7NIATv7_g23718.t1 NbV1Ch10 100.000 31 0 0
>> 405 435 12942669 12942761 1.14e-28
>> 67.8NIATv7_g23718.t1 NbV1Ch10 97.500 40 1 0
>> 171 210 12938519 12938638 4.58e-16
>> 87.8NIATv7_g23718.t1 NbV1Ch10 81.818 11 2 0
>> 161 171 12938374 12938406 4.58e-16
>> 22.3NIATv7_g23718.t1 NbV1Ch10 83.333 48 8 0
>> 271 318 12939766 12939909 2.79e-15
>> 86.7NIATv7_g23718.t1 NbV1Ch10 94.737 38 2 0
>> 33 70 12931492 12931605 2.30e-13
>> 80.5NIATv7_g23718.t1 NbV1Ch10 82.857 35 6 0
>> 251 285 12939588 12939692 5.41e-09
>> 66.2NIATv7_g23718.t1 NbV1Ch10 100.000 31 0 0
>> 317 347 12940034 12940126 1.12e-08
>> 65.1NIATv7_g23718.t1 NbV1Ch10 96.970 33 1 0
>> 1 33 12931031 12931129 1.22e-08
>> 65.1NIATv7_g23718.t1 NbV1Ch10 75.000 40 10 0
>> 336 375 12940960 12941079 1.07e-07
>> 62.0NIATv7_g23718.t1 NbV1Ch10 100.000 29 0 0
>> 223 251 12938772 12938858 3.82e-07
>> 60.1NIATv7_g23718.t1 NbV1Ch10 95.652 23 1 0
>> 70 92 12932440 12932508 0.014
>> 45.1NIATv7_g23718.t1 NbV1Ch01 80.000 60 12 0
>> 473 532 135384227 135384048 2.25e-37
>> 96.3NIATv7_g23718.t1 NbV1Ch01 82.692 52 9 0
>> 529 580 135383956 135383801 2.25e-37
>> 85.9NIATv7_g23718.t1 NbV1Ch01 92.683 41 3 0
>> 122 162 135393270 135393148 1.89e-27
>> 82.8NIATv7_g23718.t1 NbV1Ch01 90.625 32 3 0
>> 92 123 135393437 135393342 1.89e-27
>> 65.5NIATv7_g23718.t1 NbV1Ch01 73.626 91 20 3
>> 595 682 135374896 135374627 1.62e-22
>> 110NIATv7_g23718.t1 NbV1Ch01 72.500 40 11 0
>> 31 70 135399457 135399338 7.51e-21 67.8*
>>
>> Next, I ran the below command which is part of BioPerl in order to
>> generate a gff3 file for Jbrowse:
>>
>> *bp_search2gff.pl <http://bp_search2gff.pl> --in all-tblastn.1000.out
>> --out all-tblastn.gff3 --version 3 -f blast --match --source
>> tBLASTn.NitVsNb --type hit*
>>
>> However, the command has generated an empty file. Did I use command
>> wrongly or is there another way to add Blast tracks to JBrowse?
>>
>> Thank you in advance,
>>
>> Michal
>>
>>
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
|
|
From: Colin <col...@gm...> - 2019-08-29 16:54:52
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My usage of the bp_search2gff command has been like this https://www.biostars.org/p/277/#171458 Query step blastn -query query.fa -db blast.fa > blast.txt Run bp_search2gff.pl bp_search2gff.pl --input blast.txt --addid --version 3 --type hit -Colin On Thu, Aug 29, 2019 at 10:46 AM Michał T. Lorenc <m.t...@gm...> wrote: > Hi all, > I ran tblastn and have got this Blast output: > > > > > > > > > > > > > > > > > > > > > > > *NIATv7_g23718.t1 NbV1Ch10 95.789 95 4 0 > 596 690 12945534 12945818 2.55e-49 > 193NIATv7_g23718.t1 NbV1Ch10 70.290 138 4 1 > 473 573 12943183 12943596 9.76e-46 > 182NIATv7_g23718.t1 NbV1Ch10 70.290 138 4 1 > 472 572 12943180 12943593 1.36e-44 > 179NIATv7_g23718.t1 NbV1Ch10 97.561 41 1 0 > 122 162 12937586 12937708 1.02e-29 > 85.5NIATv7_g23718.t1 NbV1Ch10 93.939 33 2 0 > 91 123 12937413 12937511 1.02e-29 > 70.9NIATv7_g23718.t1 NbV1Ch10 91.111 45 4 0 > 435 479 12942868 12943002 1.14e-28 > 84.7NIATv7_g23718.t1 NbV1Ch10 100.000 31 0 0 > 405 435 12942669 12942761 1.14e-28 > 67.8NIATv7_g23718.t1 NbV1Ch10 97.500 40 1 0 > 171 210 12938519 12938638 4.58e-16 > 87.8NIATv7_g23718.t1 NbV1Ch10 81.818 11 2 0 > 161 171 12938374 12938406 4.58e-16 > 22.3NIATv7_g23718.t1 NbV1Ch10 83.333 48 8 0 > 271 318 12939766 12939909 2.79e-15 > 86.7NIATv7_g23718.t1 NbV1Ch10 94.737 38 2 0 > 33 70 12931492 12931605 2.30e-13 > 80.5NIATv7_g23718.t1 NbV1Ch10 82.857 35 6 0 > 251 285 12939588 12939692 5.41e-09 > 66.2NIATv7_g23718.t1 NbV1Ch10 100.000 31 0 0 > 317 347 12940034 12940126 1.12e-08 > 65.1NIATv7_g23718.t1 NbV1Ch10 96.970 33 1 0 > 1 33 12931031 12931129 1.22e-08 > 65.1NIATv7_g23718.t1 NbV1Ch10 75.000 40 10 0 > 336 375 12940960 12941079 1.07e-07 > 62.0NIATv7_g23718.t1 NbV1Ch10 100.000 29 0 0 > 223 251 12938772 12938858 3.82e-07 > 60.1NIATv7_g23718.t1 NbV1Ch10 95.652 23 1 0 > 70 92 12932440 12932508 0.014 > 45.1NIATv7_g23718.t1 NbV1Ch01 80.000 60 12 0 > 473 532 135384227 135384048 2.25e-37 > 96.3NIATv7_g23718.t1 NbV1Ch01 82.692 52 9 0 > 529 580 135383956 135383801 2.25e-37 > 85.9NIATv7_g23718.t1 NbV1Ch01 92.683 41 3 0 > 122 162 135393270 135393148 1.89e-27 > 82.8NIATv7_g23718.t1 NbV1Ch01 90.625 32 3 0 > 92 123 135393437 135393342 1.89e-27 > 65.5NIATv7_g23718.t1 NbV1Ch01 73.626 91 20 3 > 595 682 135374896 135374627 1.62e-22 > 110NIATv7_g23718.t1 NbV1Ch01 72.500 40 11 0 > 31 70 135399457 135399338 7.51e-21 67.8* > > Next, I ran the below command which is part of BioPerl in order to > generate a gff3 file for Jbrowse: > > *bp_search2gff.pl <http://bp_search2gff.pl> --in all-tblastn.1000.out > --out all-tblastn.gff3 --version 3 -f blast --match --source > tBLASTn.NitVsNb --type hit* > > However, the command has generated an empty file. Did I use command > wrongly or is there another way to add Blast tracks to JBrowse? > > Thank you in advance, > > Michal > > > > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Michał T. L. <m.t...@gm...> - 2019-08-29 14:46:43
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Hi all, I ran tblastn and have got this Blast output: *NIATv7_g23718.t1 NbV1Ch10 95.789 95 4 0 596 690 12945534 12945818 2.55e-49 193NIATv7_g23718.t1 NbV1Ch10 70.290 138 4 1 473 573 12943183 12943596 9.76e-46 182NIATv7_g23718.t1 NbV1Ch10 70.290 138 4 1 472 572 12943180 12943593 1.36e-44 179NIATv7_g23718.t1 NbV1Ch10 97.561 41 1 0 122 162 12937586 12937708 1.02e-29 85.5NIATv7_g23718.t1 NbV1Ch10 93.939 33 2 0 91 123 12937413 12937511 1.02e-29 70.9NIATv7_g23718.t1 NbV1Ch10 91.111 45 4 0 435 479 12942868 12943002 1.14e-28 84.7NIATv7_g23718.t1 NbV1Ch10 100.000 31 0 0 405 435 12942669 12942761 1.14e-28 67.8NIATv7_g23718.t1 NbV1Ch10 97.500 40 1 0 171 210 12938519 12938638 4.58e-16 87.8NIATv7_g23718.t1 NbV1Ch10 81.818 11 2 0 161 171 12938374 12938406 4.58e-16 22.3NIATv7_g23718.t1 NbV1Ch10 83.333 48 8 0 271 318 12939766 12939909 2.79e-15 86.7NIATv7_g23718.t1 NbV1Ch10 94.737 38 2 0 33 70 12931492 12931605 2.30e-13 80.5NIATv7_g23718.t1 NbV1Ch10 82.857 35 6 0 251 285 12939588 12939692 5.41e-09 66.2NIATv7_g23718.t1 NbV1Ch10 100.000 31 0 0 317 347 12940034 12940126 1.12e-08 65.1NIATv7_g23718.t1 NbV1Ch10 96.970 33 1 0 1 33 12931031 12931129 1.22e-08 65.1NIATv7_g23718.t1 NbV1Ch10 75.000 40 10 0 336 375 12940960 12941079 1.07e-07 62.0NIATv7_g23718.t1 NbV1Ch10 100.000 29 0 0 223 251 12938772 12938858 3.82e-07 60.1NIATv7_g23718.t1 NbV1Ch10 95.652 23 1 0 70 92 12932440 12932508 0.014 45.1NIATv7_g23718.t1 NbV1Ch01 80.000 60 12 0 473 532 135384227 135384048 2.25e-37 96.3NIATv7_g23718.t1 NbV1Ch01 82.692 52 9 0 529 580 135383956 135383801 2.25e-37 85.9NIATv7_g23718.t1 NbV1Ch01 92.683 41 3 0 122 162 135393270 135393148 1.89e-27 82.8NIATv7_g23718.t1 NbV1Ch01 90.625 32 3 0 92 123 135393437 135393342 1.89e-27 65.5NIATv7_g23718.t1 NbV1Ch01 73.626 91 20 3 595 682 135374896 135374627 1.62e-22 110NIATv7_g23718.t1 NbV1Ch01 72.500 40 11 0 31 70 135399457 135399338 7.51e-21 67.8* Next, I ran the below command which is part of BioPerl in order to generate a gff3 file for Jbrowse: *bp_search2gff.pl <http://bp_search2gff.pl> --in all-tblastn.1000.out --out all-tblastn.gff3 --version 3 -f blast --match --source tBLASTn.NitVsNb --type hit* However, the command has generated an empty file. Did I use command wrongly or is there another way to add Blast tracks to JBrowse? Thank you in advance, Michal |
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