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From: Jenni T. (TAU) <jen...@tu...> - 2021-05-21 11:45:59
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________________________________ Lähettäjä: Jenni Tolppanen (TAU) <jen...@tu...> Lähetetty: torstai 6. toukokuuta 2021 9.31 Vastaanottaja: Scott Cain <sc...@sc...> Aihe: VS: [Gmod-ajax] JBowse Hi, Thank you for the quick response! What should I do if I want BED files? And is it possible to obtain BED file from all the genome at once? -Jenni ________________________________ Lähettäjä: Scott Cain <sc...@sc...> Lähetetty: torstai 22. huhtikuuta 2021 23.09 Vastaanottaja: Jenni Tolppanen (TAU) <jen...@tu...> Kopio: gmo...@li... <gmo...@li...> Aihe: Re: [Gmod-ajax] JBowse Hi Jenni, That is very strange--I've never seen that dialog box look like that. There are two options in that box: Visible region or whole reference sequence which correspond to the two circles you can check off (with visible region selected by default and selected in the picture you sent). Even though the text is very "smooshed" the dialog box should still work, so you can select either of the circles and click "Save" and it will save a GFF3 file with the data to your computer. Please let us know if you have any problems with this, Scott On Thu, Apr 22, 2021 at 12:42 PM Jenni Tolppanen (TAU) <jen...@tu...<mailto:jen...@tu...>> wrote: Hi, I have a problem when I try to download data from the browser. For example I would like to get all common putative enhancers. Attached picture shows the problem. What should I do? Yours faithfully, Jenni Tolppanen _______________________________________________ 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: <Do...@hi...> - 2021-05-21 11:03:55
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Dear JB2 support, We have used JB1 for some of our projects before (acknowledged and cited your work properly of course), and thanks for this very useful tool! We also tried version 2 recently but found out that the following 2 features are not supported in the new version, as mentioned at https://jbrowse.org/jb2/features : Name searching e.g. ability to type a gene name/ID to search for it ❌ ✔️ URL query API e.g. specifying ?loc=chr1:1-100 in URL bar ❌ ✔️ Are they intentional (ie JB2 will never support them) or just temporary? If JB2 will never support it, is there another way to allow users quickly to jump to a specific region on a chromosome by clicking a URL? Thanks in advance! Alex. |
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From: Jeff <quj...@16...> - 2021-05-21 08:34:07
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Dear teacher， First of all, thank you very much for JBrowse, which provides great convenience for my study. One question puzzled me all the time is where is the centromere on 10 chromosomes of maize? I have read a lot of studies but it is difficult to find relevant specific information about it. I wonder if you have paid attention to the location of centromeres on the 10 chromosomes in the B73 reference genomes (version 3, 4 and 5) when sorting out the maize genome? I am looking forward to hearing from you. Best wishes, Jianzhou Qu |
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From: Garrett S. <ste...@gm...> - 2021-05-05 22:18:30
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Apollo 2.6.4 has been released: https://github.com/GMOD/Apollo/releases/tag/2.6.4 Features - Added getAttributions method 2591 <https://github.com/GMOD/Apollo/pull/2591> via @mbc32 <https://github.com/mbc32>. - Make getting track features by location optional to pull unique code 2600 <https://github.com/GMOD/Apollo/pull/2600>. - Added additional websocket authentication support 2598 <https://github.com/GMOD/Apollo/pull/2598>. - Added 'set optimal ORF' function 2129 <https://github.com/GMOD/Apollo/pull/2129>. Bug Fixes - Provide better detection and fallback for detecting proper Grails version 2020 <https://github.com/GMOD/Apollo/issues/2020>. - Bad WithOrFrom functional annotation evidence can hide display 2595 <https://github.com/GMOD/Apollo/issues/2595>. - Fixed bad API doc 2605 <https://github.com/GMOD/Apollo/issues/2605>. - Fix safari annotation panel layout 2603 <https://github.com/GMOD/Apollo/issues/2603>. Infrastructure Changes - Upgrade to JBrowse 1.16.11 <https://github.com/GMOD/jbrowse/releases/tag/1.16.11-release> - Removed server phone home 2614 <https://github.com/GMOD/Apollo/pull/2614>. Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md Docker builds are on docker hub: https://hub.docker.com/r/gmod/apollo Please review the documentation pages for more details: 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 Report issues if found. Active mailing list (ap...@lb...) and google group. |
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From: Scott C. <sc...@sc...> - 2021-05-04 21:15:49
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Don't forget to get your abstracts in for BOSC! ---------- Forwarded message --------- From: BOSC, the Bioinformatics Open Source Conference < bos...@gm...> Date: Tue, May 4, 2021 at 1:50 PM Subject: [bosc-announce] Reminder: BOSC abstract deadline is May 6! To: <bos...@go...> <https://www.open-bio.org/events/bosc/> The BOSC 2021 abstract submission <https://www.open-bio.org/events/bosc-2021/submit/> deadline is May 6th; see our announcement <https://www.open-bio.org/2021/03/24/join-us-at-bosc-2021/> for more info. This year’s BOSC is a track of ISMB/ECCB 2021 online <https://www.iscb.org/ismbeccb2021/>. What time on May 6th is the deadline? The official ISMB/ECCB deadline is 11:59pm EDT on May 6 (which is 03:59 UTC on May 7), but we convinced them to let us keep submissions for BOSC open until 11:59pm Hawaii time (which is six hours later, 09:59 UTC on May 7). We are unfortunately unable to grant any additional extensions. Late Poster deadline is June 3. If you can’t make the May 6th submission deadline, we encourage you to submit for a Late Poster (deadline June 3). As space permits, we will choose a few Late Poster submissions for Late-Breaking Lightning Talks. Fee assistance. Just check a box on the abstract submission form to request registration fee assistance! Join us on Slack! Our BOSC Slack workspace <https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew> is open to the community! Follow us on Twitter! @OBF_BOSC <http://twitter.com/OBF_BOSC>, #BOSC2021 -- You received this message because you are subscribed to the Google Groups "bosc-announce" group. To unsubscribe from this group and stop receiving emails from it, send an email to bos...@go.... To view this discussion on the web visit https://groups.google.com/d/msgid/bosc-announce/CAK27n1fyqV9KP1pR%2BOdYh%3D5rW%2BGdah-KQPJajCUxMMKXgqADZQ%40mail.gmail.com <https://groups.google.com/d/msgid/bosc-announce/CAK27n1fyqV9KP1pR%2BOdYh%3D5rW%2BGdah-KQPJajCUxMMKXgqADZQ%40mail.gmail.com?utm_medium=email&utm_source=footer> . -- ------------------------------------------------------------------------ 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: Colin <col...@gm...> - 2021-04-30 19:05:47
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The blue corresponds to negative strand and brown to positive strand, which matches up with in the screenshot that it is brown matching the positive strand gene, blue with negativetsas I updated the README of the plugin to try to help clarify that -Colin On Fri, Apr 30, 2021 at 12:03 PM Hans Vasquez-Gross < hav...@uc...> wrote: > Hi Colin, > > Thank you, re-running setup.sh did the trick. > > I got a question regarding SashimiPlot. I know the opacity of the line is > a measurement of number of reads that support the junction point. However, > do the different colors signify anything? I'm guessing it just switches > between blue/brown to easily distinguish between different genes? > > [image: Screenshot from 2021-04-30 08-58-04.png] > > > Thank you, > -Hans > > On Thu, Apr 29, 2021 at 6:07 PM Colin <col...@gm...> wrote: > >> You may need to re-run setup.sh after downloading SashimiPlot to the >> plugins/SashimiPlot folder >> >> Another faq entry to help explain... >> https://jbrowse.org/docs/faq.html#how-do-i-use-plugins-with-jbrowse >> >> Hope that helps :) >> -Colin >> >> On Thu, Apr 29, 2021 at 8:48 PM Hans Vasquez-Gross via Gmod-ajax < >> gmo...@li...> wrote: >> >>> Hi JBrowse team, >>> >>> I am trying to install SashimiPlot plugin in JBrowse. I already have >>> another plugin enabled on JBrowse (VariantEffectPlugin), so plugins are >>> generally working. I performed the same steps to enable it. >>> >>> 1) In the plugins folder, cloned the git repo >>> 2) Renamed git folder from sashimiplot to SashimiPlot >>> 3) Added configuration to jbrowse.conf >>> >>> [ plugins.SashimiPlot ] >>> location = plugins/SashimiPlot >>> [ plugins.VariantEffectPlugin ] >>> location = plugins/VariantEffectPlugin >>> >>> 4) Added track configuration to tracks.conf >>> >>> [tracks.pachon_adult_ovary_rep2_bam] >>> urlTemplate=pachon_adult_ovary_n7.rep2.sorted.bam >>> storeClass=JBrowse/Store/SeqFeature/BAM >>> type=SashimiPlot/View/Track/Sashimi >>> chunkSizeLimit = 50000000 >>> useXS = true >>> category = Sashimi >>> label = Pachon Adult Ovary rep2 sashimi >>> >>> >>> The result is the following screenshot. >>> [image: Screenshot from 2021-04-29 17-40-44.png] >>> >>> >>> Did I do something wrong during the installation? >>> >>> Thank you, >>> -Hans >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> > > -- > Hans Vasquez-Gross > <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> > PhD Candidate > Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ > Department of Plant Science > University of California at Davis > Email: hav...@uc... > Skype: hansvg.ucd > |
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From: Hans Vasquez-G. <hav...@uc...> - 2021-04-30 16:03:38
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Hi Colin, Thank you, re-running setup.sh did the trick. I got a question regarding SashimiPlot. I know the opacity of the line is a measurement of number of reads that support the junction point. However, do the different colors signify anything? I'm guessing it just switches between blue/brown to easily distinguish between different genes? [image: Screenshot from 2021-04-30 08-58-04.png] Thank you, -Hans On Thu, Apr 29, 2021 at 6:07 PM Colin <col...@gm...> wrote: > You may need to re-run setup.sh after downloading SashimiPlot to the > plugins/SashimiPlot folder > > Another faq entry to help explain... > https://jbrowse.org/docs/faq.html#how-do-i-use-plugins-with-jbrowse > > Hope that helps :) > -Colin > > On Thu, Apr 29, 2021 at 8:48 PM Hans Vasquez-Gross via Gmod-ajax < > gmo...@li...> wrote: > >> Hi JBrowse team, >> >> I am trying to install SashimiPlot plugin in JBrowse. I already have >> another plugin enabled on JBrowse (VariantEffectPlugin), so plugins are >> generally working. I performed the same steps to enable it. >> >> 1) In the plugins folder, cloned the git repo >> 2) Renamed git folder from sashimiplot to SashimiPlot >> 3) Added configuration to jbrowse.conf >> >> [ plugins.SashimiPlot ] >> location = plugins/SashimiPlot >> [ plugins.VariantEffectPlugin ] >> location = plugins/VariantEffectPlugin >> >> 4) Added track configuration to tracks.conf >> >> [tracks.pachon_adult_ovary_rep2_bam] >> urlTemplate=pachon_adult_ovary_n7.rep2.sorted.bam >> storeClass=JBrowse/Store/SeqFeature/BAM >> type=SashimiPlot/View/Track/Sashimi >> chunkSizeLimit = 50000000 >> useXS = true >> category = Sashimi >> label = Pachon Adult Ovary rep2 sashimi >> >> >> The result is the following screenshot. >> [image: Screenshot from 2021-04-29 17-40-44.png] >> >> >> Did I do something wrong during the installation? >> >> Thank you, >> -Hans >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > -- Hans Vasquez-Gross <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> PhD Candidate Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ Department of Plant Science University of California at Davis Email: hav...@uc... Skype: hansvg.ucd |
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From: Colin <col...@gm...> - 2021-04-30 01:08:00
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You may need to re-run setup.sh after downloading SashimiPlot to the plugins/SashimiPlot folder Another faq entry to help explain... https://jbrowse.org/docs/faq.html#how-do-i-use-plugins-with-jbrowse Hope that helps :) -Colin On Thu, Apr 29, 2021 at 8:48 PM Hans Vasquez-Gross via Gmod-ajax < gmo...@li...> wrote: > Hi JBrowse team, > > I am trying to install SashimiPlot plugin in JBrowse. I already have > another plugin enabled on JBrowse (VariantEffectPlugin), so plugins are > generally working. I performed the same steps to enable it. > > 1) In the plugins folder, cloned the git repo > 2) Renamed git folder from sashimiplot to SashimiPlot > 3) Added configuration to jbrowse.conf > > [ plugins.SashimiPlot ] > location = plugins/SashimiPlot > [ plugins.VariantEffectPlugin ] > location = plugins/VariantEffectPlugin > > 4) Added track configuration to tracks.conf > > [tracks.pachon_adult_ovary_rep2_bam] > urlTemplate=pachon_adult_ovary_n7.rep2.sorted.bam > storeClass=JBrowse/Store/SeqFeature/BAM > type=SashimiPlot/View/Track/Sashimi > chunkSizeLimit = 50000000 > useXS = true > category = Sashimi > label = Pachon Adult Ovary rep2 sashimi > > > The result is the following screenshot. > [image: Screenshot from 2021-04-29 17-40-44.png] > > > Did I do something wrong during the installation? > > Thank you, > -Hans > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Hans Vasquez-G. <hav...@uc...> - 2021-04-30 00:48:21
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Hi JBrowse team, I am trying to install SashimiPlot plugin in JBrowse. I already have another plugin enabled on JBrowse (VariantEffectPlugin), so plugins are generally working. I performed the same steps to enable it. 1) In the plugins folder, cloned the git repo 2) Renamed git folder from sashimiplot to SashimiPlot 3) Added configuration to jbrowse.conf [ plugins.SashimiPlot ] location = plugins/SashimiPlot [ plugins.VariantEffectPlugin ] location = plugins/VariantEffectPlugin 4) Added track configuration to tracks.conf [tracks.pachon_adult_ovary_rep2_bam] urlTemplate=pachon_adult_ovary_n7.rep2.sorted.bam storeClass=JBrowse/Store/SeqFeature/BAM type=SashimiPlot/View/Track/Sashimi chunkSizeLimit = 50000000 useXS = true category = Sashimi label = Pachon Adult Ovary rep2 sashimi The result is the following screenshot. [image: Screenshot from 2021-04-29 17-40-44.png] Did I do something wrong during the installation? Thank you, -Hans |
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From: Hans Vasquez-G. <hav...@uc...> - 2021-04-29 22:05:39
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Thank you Colin. Adding subparts to my .conf did the trick. All the best, Hans On Thu, Apr 29, 2021, 2:58 PM Colin <col...@gm...> wrote: > Here are a couple tips that may help > > > https://jbrowse.org/docs/faq.html#my-canvasfeatures-don-t-show-up-with-subfeatures-why-not > > The first rule, that you must set transcriptType, was relaxed in recent > versions so adding subParts: "exon" should be sufficient > > -Colin > > On Thu, Apr 29, 2021 at 5:43 PM Hans Vasquez-Gross via Gmod-ajax < > gmo...@li...> wrote: > >> Hi JBrowse Team, >> >> I have two GFFs, both which have been converted from GTF using gff read >> then gt gff3 to sort. However, one of my GFF files is not displaying exons >> on the browser. It is only displaying the transcript line but not the exon >> boundaries. >> >> [image: Screenshot from 2021-04-29 14-35-34.png] >> >> The second track I used stringtie to generate a merged GTF track from an >> RNAseq project. However, it doesn't seem to define CDS, only transcript and >> exons. Could this be the source of the problem? >> >> Below I'll give an excerpt of each GFF file: >> *1st working GFF* >> # gffread -E Astyanax_mexicanus.Astyanax_mexicanus-2.0.103.gtf -o- >> # gffread v0.11.7 >> 1 ensembl exon 19172 19231 . - . >> Parent=ENSAMXT00000042139 >> 1 ensembl CDS 19172 19231 . - 0 >> Parent=ENSAMXT00000042139 >> 1 ensembl transcript 19172 27555 . - . >> ID=ENSAMXT00000042139;geneID=ENSAMXG00000035673 >> 1 ensembl exon 19778 20349 . - . >> Parent=ENSAMXT00000037267 >> 1 ensembl transcript 19778 27555 . - . >> ID=ENSAMXT00000037267;geneID=ENSAMXG00000035673 >> 1 ensembl CDS 20212 20349 . - 0 >> Parent=ENSAMXT00000037267 >> 1 ensembl exon 20281 20349 . - . >> Parent=ENSAMXT00000042139 >> 1 ensembl CDS 20281 20349 . - 0 >> Parent=ENSAMXT00000042139 >> 1 ensembl CDS 21829 21981 . - 0 >> Parent=ENSAMXT00000042139 >> 1 ensembl CDS 21829 21981 . - 0 >> Parent=ENSAMXT00000037267 >> 1 ensembl exon 21829 21981 . - . >> Parent=ENSAMXT00000037267 >> 1 ensembl exon 21829 21981 . - . >> Parent=ENSAMXT00000042139 >> 1 ensembl CDS 22129 22218 . - 0 >> Parent=ENSAMXT00000042139 >> 1 ensembl exon 22129 22218 . - . >> Parent=ENSAMXT00000042139 >> 1 ensembl exon 22129 22218 . - . >> Parent=ENSAMXT00000037267 >> 1 ensembl CDS 22129 22218 . - 0 >> Parent=ENSAMXT00000037267 >> 1 ensembl CDS 23160 23234 . - 0 >> Parent=ENSAMXT00000042139 >> 1 ensembl exon 23160 23234 . - . >> Parent=ENSAMXT00000042139 >> 1 ensembl exon 23160 23234 . - . >> Parent=ENSAMXT00000037267 >> 1 ensembl CDS 23160 23234 . - 0 >> Parent=ENSAMXT00000037267 >> 1 ensembl CDS 24621 24803 . - 0 >> Parent=ENSAMXT00000037267 >> 1 ensembl CDS 24621 24803 . - 0 >> Parent=ENSAMXT00000042139 >> 1 ensembl exon 24621 24803 . - . >> Parent=ENSAMXT00000042139 >> 1 ensembl exon 24621 24803 . - . >> Parent=ENSAMXT00000037267 >> 1 ensembl CDS 27412 27555 . - 0 >> Parent=ENSAMXT00000037267 >> 1 ensembl CDS 27412 27555 . - 0 >> Parent=ENSAMXT00000042139 >> 1 ensembl exon 27412 27555 . - . >> Parent=ENSAMXT00000042139 >> 1 ensembl exon 27412 27555 . - . >> Parent=ENSAMXT00000037267 >> >> >> *2nd non-working GFF* >> # gffread -E merged.gtf -o- >> # gffread v0.11.7 >> 1 StringTie exon 19172 19231 1e+03 - . >> Parent=ENSAMXT00000042139 >> 1 StringTie transcript 19172 27555 1e+03 - . >> ID=ENSAMXT00000042139;geneID=MSTRG.2 >> 1 StringTie exon 19778 20349 1e+03 - . >> Parent=ENSAMXT00000037267 >> 1 StringTie transcript 19778 27555 1e+03 - . >> ID=ENSAMXT00000037267;geneID=MSTRG.2 >> 1 StringTie exon 20281 20349 1e+03 - . >> Parent=ENSAMXT00000042139 >> 1 StringTie exon 21829 21981 1e+03 - . >> Parent=ENSAMXT00000037267 >> 1 StringTie exon 21829 21981 1e+03 - . >> Parent=ENSAMXT00000042139 >> 1 StringTie exon 22129 22218 1e+03 - . >> Parent=ENSAMXT00000037267 >> 1 StringTie exon 22129 22218 1e+03 - . >> Parent=ENSAMXT00000042139 >> 1 StringTie exon 23160 23234 1e+03 - . >> Parent=ENSAMXT00000042139 >> 1 StringTie exon 23160 23234 1e+03 - . >> Parent=ENSAMXT00000037267 >> 1 StringTie exon 24621 24803 1e+03 - . >> Parent=ENSAMXT00000037267 >> 1 StringTie exon 24621 24803 1e+03 - . >> Parent=ENSAMXT00000042139 >> 1 StringTie exon 27412 27555 1e+03 - . >> Parent=ENSAMXT00000042139 >> 1 StringTie exon 27412 27555 1e+03 - . >> Parent=ENSAMXT00000037267 >> ### >> >> Do you have any suggestions on how to get the second GFF displaying >> properly with exon boundaries on the transcript line? >> >> Thank you, >> -Hans >> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
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From: Colin <col...@gm...> - 2021-04-29 21:58:25
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Here are a couple tips that may help https://jbrowse.org/docs/faq.html#my-canvasfeatures-don-t-show-up-with-subfeatures-why-not The first rule, that you must set transcriptType, was relaxed in recent versions so adding subParts: "exon" should be sufficient -Colin On Thu, Apr 29, 2021 at 5:43 PM Hans Vasquez-Gross via Gmod-ajax < gmo...@li...> wrote: > Hi JBrowse Team, > > I have two GFFs, both which have been converted from GTF using gff read > then gt gff3 to sort. However, one of my GFF files is not displaying exons > on the browser. It is only displaying the transcript line but not the exon > boundaries. > > [image: Screenshot from 2021-04-29 14-35-34.png] > > The second track I used stringtie to generate a merged GTF track from an > RNAseq project. However, it doesn't seem to define CDS, only transcript and > exons. Could this be the source of the problem? > > Below I'll give an excerpt of each GFF file: > *1st working GFF* > # gffread -E Astyanax_mexicanus.Astyanax_mexicanus-2.0.103.gtf -o- > # gffread v0.11.7 > 1 ensembl exon 19172 19231 . - . > Parent=ENSAMXT00000042139 > 1 ensembl CDS 19172 19231 . - 0 > Parent=ENSAMXT00000042139 > 1 ensembl transcript 19172 27555 . - . > ID=ENSAMXT00000042139;geneID=ENSAMXG00000035673 > 1 ensembl exon 19778 20349 . - . > Parent=ENSAMXT00000037267 > 1 ensembl transcript 19778 27555 . - . > ID=ENSAMXT00000037267;geneID=ENSAMXG00000035673 > 1 ensembl CDS 20212 20349 . - 0 > Parent=ENSAMXT00000037267 > 1 ensembl exon 20281 20349 . - . > Parent=ENSAMXT00000042139 > 1 ensembl CDS 20281 20349 . - 0 > Parent=ENSAMXT00000042139 > 1 ensembl CDS 21829 21981 . - 0 > Parent=ENSAMXT00000042139 > 1 ensembl CDS 21829 21981 . - 0 > Parent=ENSAMXT00000037267 > 1 ensembl exon 21829 21981 . - . > Parent=ENSAMXT00000037267 > 1 ensembl exon 21829 21981 . - . > Parent=ENSAMXT00000042139 > 1 ensembl CDS 22129 22218 . - 0 > Parent=ENSAMXT00000042139 > 1 ensembl exon 22129 22218 . - . > Parent=ENSAMXT00000042139 > 1 ensembl exon 22129 22218 . - . > Parent=ENSAMXT00000037267 > 1 ensembl CDS 22129 22218 . - 0 > Parent=ENSAMXT00000037267 > 1 ensembl CDS 23160 23234 . - 0 > Parent=ENSAMXT00000042139 > 1 ensembl exon 23160 23234 . - . > Parent=ENSAMXT00000042139 > 1 ensembl exon 23160 23234 . - . > Parent=ENSAMXT00000037267 > 1 ensembl CDS 23160 23234 . - 0 > Parent=ENSAMXT00000037267 > 1 ensembl CDS 24621 24803 . - 0 > Parent=ENSAMXT00000037267 > 1 ensembl CDS 24621 24803 . - 0 > Parent=ENSAMXT00000042139 > 1 ensembl exon 24621 24803 . - . > Parent=ENSAMXT00000042139 > 1 ensembl exon 24621 24803 . - . > Parent=ENSAMXT00000037267 > 1 ensembl CDS 27412 27555 . - 0 > Parent=ENSAMXT00000037267 > 1 ensembl CDS 27412 27555 . - 0 > Parent=ENSAMXT00000042139 > 1 ensembl exon 27412 27555 . - . > Parent=ENSAMXT00000042139 > 1 ensembl exon 27412 27555 . - . > Parent=ENSAMXT00000037267 > > > *2nd non-working GFF* > # gffread -E merged.gtf -o- > # gffread v0.11.7 > 1 StringTie exon 19172 19231 1e+03 - . > Parent=ENSAMXT00000042139 > 1 StringTie transcript 19172 27555 1e+03 - . > ID=ENSAMXT00000042139;geneID=MSTRG.2 > 1 StringTie exon 19778 20349 1e+03 - . > Parent=ENSAMXT00000037267 > 1 StringTie transcript 19778 27555 1e+03 - . > ID=ENSAMXT00000037267;geneID=MSTRG.2 > 1 StringTie exon 20281 20349 1e+03 - . > Parent=ENSAMXT00000042139 > 1 StringTie exon 21829 21981 1e+03 - . > Parent=ENSAMXT00000037267 > 1 StringTie exon 21829 21981 1e+03 - . > Parent=ENSAMXT00000042139 > 1 StringTie exon 22129 22218 1e+03 - . > Parent=ENSAMXT00000037267 > 1 StringTie exon 22129 22218 1e+03 - . > Parent=ENSAMXT00000042139 > 1 StringTie exon 23160 23234 1e+03 - . > Parent=ENSAMXT00000042139 > 1 StringTie exon 23160 23234 1e+03 - . > Parent=ENSAMXT00000037267 > 1 StringTie exon 24621 24803 1e+03 - . > Parent=ENSAMXT00000037267 > 1 StringTie exon 24621 24803 1e+03 - . > Parent=ENSAMXT00000042139 > 1 StringTie exon 27412 27555 1e+03 - . > Parent=ENSAMXT00000042139 > 1 StringTie exon 27412 27555 1e+03 - . > Parent=ENSAMXT00000037267 > ### > > Do you have any suggestions on how to get the second GFF displaying > properly with exon boundaries on the transcript line? > > Thank you, > -Hans > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Hans Vasquez-G. <hav...@uc...> - 2021-04-29 21:42:51
|
Hi JBrowse Team,
I have two GFFs, both which have been converted from GTF using gff read
then gt gff3 to sort. However, one of my GFF files is not displaying exons
on the browser. It is only displaying the transcript line but not the exon
boundaries.
[image: Screenshot from 2021-04-29 14-35-34.png]
The second track I used stringtie to generate a merged GTF track from an
RNAseq project. However, it doesn't seem to define CDS, only transcript and
exons. Could this be the source of the problem?
Below I'll give an excerpt of each GFF file:
*1st working GFF*
# gffread -E Astyanax_mexicanus.Astyanax_mexicanus-2.0.103.gtf -o-
# gffread v0.11.7
1 ensembl exon 19172 19231 . - .
Parent=ENSAMXT00000042139
1 ensembl CDS 19172 19231 . - 0
Parent=ENSAMXT00000042139
1 ensembl transcript 19172 27555 . - .
ID=ENSAMXT00000042139;geneID=ENSAMXG00000035673
1 ensembl exon 19778 20349 . - .
Parent=ENSAMXT00000037267
1 ensembl transcript 19778 27555 . - .
ID=ENSAMXT00000037267;geneID=ENSAMXG00000035673
1 ensembl CDS 20212 20349 . - 0
Parent=ENSAMXT00000037267
1 ensembl exon 20281 20349 . - .
Parent=ENSAMXT00000042139
1 ensembl CDS 20281 20349 . - 0
Parent=ENSAMXT00000042139
1 ensembl CDS 21829 21981 . - 0
Parent=ENSAMXT00000042139
1 ensembl CDS 21829 21981 . - 0
Parent=ENSAMXT00000037267
1 ensembl exon 21829 21981 . - .
Parent=ENSAMXT00000037267
1 ensembl exon 21829 21981 . - .
Parent=ENSAMXT00000042139
1 ensembl CDS 22129 22218 . - 0
Parent=ENSAMXT00000042139
1 ensembl exon 22129 22218 . - .
Parent=ENSAMXT00000042139
1 ensembl exon 22129 22218 . - .
Parent=ENSAMXT00000037267
1 ensembl CDS 22129 22218 . - 0
Parent=ENSAMXT00000037267
1 ensembl CDS 23160 23234 . - 0
Parent=ENSAMXT00000042139
1 ensembl exon 23160 23234 . - .
Parent=ENSAMXT00000042139
1 ensembl exon 23160 23234 . - .
Parent=ENSAMXT00000037267
1 ensembl CDS 23160 23234 . - 0
Parent=ENSAMXT00000037267
1 ensembl CDS 24621 24803 . - 0
Parent=ENSAMXT00000037267
1 ensembl CDS 24621 24803 . - 0
Parent=ENSAMXT00000042139
1 ensembl exon 24621 24803 . - .
Parent=ENSAMXT00000042139
1 ensembl exon 24621 24803 . - .
Parent=ENSAMXT00000037267
1 ensembl CDS 27412 27555 . - 0
Parent=ENSAMXT00000037267
1 ensembl CDS 27412 27555 . - 0
Parent=ENSAMXT00000042139
1 ensembl exon 27412 27555 . - .
Parent=ENSAMXT00000042139
1 ensembl exon 27412 27555 . - .
Parent=ENSAMXT00000037267
*2nd non-working GFF*
# gffread -E merged.gtf -o-
# gffread v0.11.7
1 StringTie exon 19172 19231 1e+03 - .
Parent=ENSAMXT00000042139
1 StringTie transcript 19172 27555 1e+03 - .
ID=ENSAMXT00000042139;geneID=MSTRG.2
1 StringTie exon 19778 20349 1e+03 - .
Parent=ENSAMXT00000037267
1 StringTie transcript 19778 27555 1e+03 - .
ID=ENSAMXT00000037267;geneID=MSTRG.2
1 StringTie exon 20281 20349 1e+03 - .
Parent=ENSAMXT00000042139
1 StringTie exon 21829 21981 1e+03 - .
Parent=ENSAMXT00000037267
1 StringTie exon 21829 21981 1e+03 - .
Parent=ENSAMXT00000042139
1 StringTie exon 22129 22218 1e+03 - .
Parent=ENSAMXT00000037267
1 StringTie exon 22129 22218 1e+03 - .
Parent=ENSAMXT00000042139
1 StringTie exon 23160 23234 1e+03 - .
Parent=ENSAMXT00000042139
1 StringTie exon 23160 23234 1e+03 - .
Parent=ENSAMXT00000037267
1 StringTie exon 24621 24803 1e+03 - .
Parent=ENSAMXT00000037267
1 StringTie exon 24621 24803 1e+03 - .
Parent=ENSAMXT00000042139
1 StringTie exon 27412 27555 1e+03 - .
Parent=ENSAMXT00000042139
1 StringTie exon 27412 27555 1e+03 - .
Parent=ENSAMXT00000037267
###
Do you have any suggestions on how to get the second GFF displaying
properly with exon boundaries on the transcript line?
Thank you,
-Hans
|
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From: Scott C. <sc...@sc...> - 2021-04-22 20:15:34
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Hi Jenni, That is very strange--I've never seen that dialog box look like that. There are two options in that box: Visible region or whole reference sequence which correspond to the two circles you can check off (with visible region selected by default and selected in the picture you sent). Even though the text is very "smooshed" the dialog box should still work, so you can select either of the circles and click "Save" and it will save a GFF3 file with the data to your computer. Please let us know if you have any problems with this, Scott On Thu, Apr 22, 2021 at 12:42 PM Jenni Tolppanen (TAU) < jen...@tu...> wrote: > Hi, > > I have a problem when I try to download data from the browser. For example > I would like to get all common putative enhancers. Attached picture shows > the problem. What should I do? > > Yours faithfully, > > Jenni Tolppanen > _______________________________________________ > 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: Jenni T. (TAU) <jen...@tu...> - 2021-04-22 19:33:17
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Hi, I have a problem when I try to download data from the browser. For example I would like to get all common putative enhancers. Attached picture shows the problem. What should I do? Yours faithfully, Jenni Tolppanen |
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From: Ke J. <bio...@gm...> - 2021-03-31 16:27:09
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Great! As long as we have unlimited JSON for the "metadata" attribute, it provides enough flexibility to incorporate metadata into the tracks. Thanks! On Wed, Mar 31, 2021 at 11:05 AM Colin <col...@gm...> wrote: > See this link as an example of how it can look in the track config > > > https://github.com/GMOD/jbrowse-components/blob/1ed6ae804c50a8b733a65a6560200d860c36f638/test_data/config_demo.json#L82-L85 > > -Colin > > On Wed, Mar 31, 2021 at 12:04 PM Colin <col...@gm...> wrote: > >> Hi Ke, >> All tracks in jbrowse 2 can have a "metadata" field that can contain >> arbitrary JSON, and this will be displayed in the "About track" dialog box >> >> There aren't any extra features like searching for tracks by metadata yet >> but there is a possible feature request for that here >> https://github.com/GMOD/jbrowse-components/issues/1708 >> >> There also aren't any special command line options to help supply >> metadata during track loading but if that would be helpful let us know >> >> -Colin >> >> On Wed, Mar 31, 2021 at 10:45 AM Ke Jiang <bio...@gm...> wrote: >> >>> Hi, >>> >>> As I'm diving deeper to JBrowse2, I'm wondering whether there is a >>> similar attribute to JBrowse "metadata" field (and the faceted track >>> selector function associated with it). Or the "category" levels are taking >>> that role. With increasing data types and volume, I'll be happy to have >>> some advice on managing tracks based on their metadata. >>> >>> Thanks! >>> >>> Ke >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> |
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From: Colin <col...@gm...> - 2021-03-31 16:05:38
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See this link as an example of how it can look in the track config https://github.com/GMOD/jbrowse-components/blob/1ed6ae804c50a8b733a65a6560200d860c36f638/test_data/config_demo.json#L82-L85 -Colin On Wed, Mar 31, 2021 at 12:04 PM Colin <col...@gm...> wrote: > Hi Ke, > All tracks in jbrowse 2 can have a "metadata" field that can contain > arbitrary JSON, and this will be displayed in the "About track" dialog box > > There aren't any extra features like searching for tracks by metadata yet > but there is a possible feature request for that here > https://github.com/GMOD/jbrowse-components/issues/1708 > > There also aren't any special command line options to help supply metadata > during track loading but if that would be helpful let us know > > -Colin > > On Wed, Mar 31, 2021 at 10:45 AM Ke Jiang <bio...@gm...> wrote: > >> Hi, >> >> As I'm diving deeper to JBrowse2, I'm wondering whether there is a >> similar attribute to JBrowse "metadata" field (and the faceted track >> selector function associated with it). Or the "category" levels are taking >> that role. With increasing data types and volume, I'll be happy to have >> some advice on managing tracks based on their metadata. >> >> Thanks! >> >> Ke >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
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From: Colin <col...@gm...> - 2021-03-31 16:04:38
|
Hi Ke, All tracks in jbrowse 2 can have a "metadata" field that can contain arbitrary JSON, and this will be displayed in the "About track" dialog box There aren't any extra features like searching for tracks by metadata yet but there is a possible feature request for that here https://github.com/GMOD/jbrowse-components/issues/1708 There also aren't any special command line options to help supply metadata during track loading but if that would be helpful let us know -Colin On Wed, Mar 31, 2021 at 10:45 AM Ke Jiang <bio...@gm...> wrote: > Hi, > > As I'm diving deeper to JBrowse2, I'm wondering whether there is a similar > attribute to JBrowse "metadata" field (and the faceted track selector > function associated with it). Or the "category" levels are taking that > role. With increasing data types and volume, I'll be happy to have some > advice on managing tracks based on their metadata. > > Thanks! > > Ke > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Ke J. <bio...@gm...> - 2021-03-31 14:45:23
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Hi, As I'm diving deeper to JBrowse2, I'm wondering whether there is a similar attribute to JBrowse "metadata" field (and the faceted track selector function associated with it). Or the "category" levels are taking that role. With increasing data types and volume, I'll be happy to have some advice on managing tracks based on their metadata. Thanks! Ke |
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From: Scott C. <sc...@sc...> - 2021-03-29 20:15:52
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And I should have added, this is covered here: https://jbrowse.org/docs/mouse_configs.html On Mon, Mar 29, 2021 at 12:14 PM Scott Cain <sc...@sc...> wrote: > Hi Hans, > > This one is pretty easy; you need the "unsafe" options: > > "unsafePopup" : true, > "unsafeMouseover" : true, > > In your example, the popup one should do the trick. > > On Mon, Mar 29, 2021 at 11:03 AM Hans Vasquez-Gross via Gmod-ajax < > gmo...@li...> wrote: > >> Also, is there a new setting to get html encoded in trask.conf or plugins >> to render? Here is an example using metadata. >> >> [ tracks.syn_a1hq ] >> storeClass = JBrowse/Store/SeqFeature/VCFTabix >> urlTemplate = syn/syn-wt_A-1.snpEff.highQ.vcf.gz >> category = VCF / Syn Ab >> #type = JBrowse/View/Track/CanvasVariants >> type = VariantEffectPlugin/View/Track/CanvasEffectVariants >> style.labelScale = 0.01 >> metadata.SNP-Colors = <span style='background-color:red'> </span> >> <span style='color:red'>(Red)</span> - SNPs with truncations<br><span >> style='background-color:purple'> </span> <span >> style='color:purple'>(Violet)</span> - amino acid changes<br><span >> style='background-color:green'> </span> <span >> style='color:green'>(Green)</span> - silent mutations<br><span >> style='background-color:blue'> </span> <span >> style='color:blue'>(Blue)</span> - outside gene regions >> key = A-1 SnpEff HQ Variants >> >> >> [image: Screen Shot 2021-03-29 at 11.01.38 AM.png] >> >> >> On Mon, Mar 29, 2021 at 9:02 AM Hans Vasquez-Gross < >> hav...@uc...> wrote: >> >>> Hi Colin, >>> >>> When we get our new webserver, I'll be setting it up so that we will >>> have a public instance. For now though, it requires connecting via >>> university VPN to load the website. >>> Here is a screenshot of the track config of the M-10 Variant >>> (non-labeled). >>> >>> [image: Screen Shot 2021-03-29 at 8.58.45 AM.png] >>> >>> >>> Best, >>> -Hans >>> >>> >>> >>> On Sun, Mar 28, 2021 at 10:57 PM Colin <col...@gm...> wrote: >>> >>>> The attribute style.labelScale=0.01 should be able to be used for >>>> forcing VCF labels to be drawn on dense tracks (e.g. >>>> https://jbrowse.org/docs/faq.html#my-track-doesn-t-display-the-gene-names-but-i-expected-it-to-why-not >>>> ) >>>> >>>> The value 0.01 corresponds to forcing labels to be drawn when you are >>>> zoomed in closer than about 100,000bp view window or so (e.g. >>>> 1000px/0.01pxPerBp=100,000bp) >>>> >>>> If you have an instance we can see that can be seen or any custom >>>> config, maybe that would help? >>>> >>>> -Colin >>>> >>>> On Fri, Mar 26, 2021 at 8:07 PM Hans Vasquez-Gross via Gmod-ajax < >>>> gmo...@li...> wrote: >>>> >>>>> Hi all, >>>>> >>>>> I want to force labels on VCF tracks. I found this on a previous >>>>> email: >>>>> >>>>> "style":{"labelScale": 0.01} >>>>> However, I dont use trackList.json for my VCF configurations, I use >>>>> tracks.conf. I tried setting it as style.labelScale = 0.01, but the labels >>>>> are still not being drawn on the track for dense tracks. >>>>> >>>>> Thank you, >>>>> -Hans >>>>> >>>>> >>>>> _______________________________________________ >>>>> Gmod-ajax mailing list >>>>> Gmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>> >>>> >>> >>> -- >>> Hans Vasquez-Gross >>> <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> >>> PhD Candidate >>> Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ >>> Department of Plant Science >>> University of California at Davis >>> Email: hav...@uc... >>> Skype: hansvg.ucd >>> >> >> >> -- >> Hans Vasquez-Gross >> <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> >> PhD Candidate >> Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ >> Department of Plant Science >> University of California at Davis >> Email: hav...@uc... >> Skype: hansvg.ucd >> _______________________________________________ >> 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: Scott C. <sc...@sc...> - 2021-03-29 19:21:53
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Hi Hans, This one is pretty easy; you need the "unsafe" options: "unsafePopup" : true, "unsafeMouseover" : true, In your example, the popup one should do the trick. On Mon, Mar 29, 2021 at 11:03 AM Hans Vasquez-Gross via Gmod-ajax < gmo...@li...> wrote: > Also, is there a new setting to get html encoded in trask.conf or plugins > to render? Here is an example using metadata. > > [ tracks.syn_a1hq ] > storeClass = JBrowse/Store/SeqFeature/VCFTabix > urlTemplate = syn/syn-wt_A-1.snpEff.highQ.vcf.gz > category = VCF / Syn Ab > #type = JBrowse/View/Track/CanvasVariants > type = VariantEffectPlugin/View/Track/CanvasEffectVariants > style.labelScale = 0.01 > metadata.SNP-Colors = <span style='background-color:red'> </span> > <span style='color:red'>(Red)</span> - SNPs with truncations<br><span > style='background-color:purple'> </span> <span > style='color:purple'>(Violet)</span> - amino acid changes<br><span > style='background-color:green'> </span> <span > style='color:green'>(Green)</span> - silent mutations<br><span > style='background-color:blue'> </span> <span > style='color:blue'>(Blue)</span> - outside gene regions > key = A-1 SnpEff HQ Variants > > > [image: Screen Shot 2021-03-29 at 11.01.38 AM.png] > > > On Mon, Mar 29, 2021 at 9:02 AM Hans Vasquez-Gross < > hav...@uc...> wrote: > >> Hi Colin, >> >> When we get our new webserver, I'll be setting it up so that we will have >> a public instance. For now though, it requires connecting via university >> VPN to load the website. >> Here is a screenshot of the track config of the M-10 Variant >> (non-labeled). >> >> [image: Screen Shot 2021-03-29 at 8.58.45 AM.png] >> >> >> Best, >> -Hans >> >> >> >> On Sun, Mar 28, 2021 at 10:57 PM Colin <col...@gm...> wrote: >> >>> The attribute style.labelScale=0.01 should be able to be used for >>> forcing VCF labels to be drawn on dense tracks (e.g. >>> https://jbrowse.org/docs/faq.html#my-track-doesn-t-display-the-gene-names-but-i-expected-it-to-why-not >>> ) >>> >>> The value 0.01 corresponds to forcing labels to be drawn when you are >>> zoomed in closer than about 100,000bp view window or so (e.g. >>> 1000px/0.01pxPerBp=100,000bp) >>> >>> If you have an instance we can see that can be seen or any custom >>> config, maybe that would help? >>> >>> -Colin >>> >>> On Fri, Mar 26, 2021 at 8:07 PM Hans Vasquez-Gross via Gmod-ajax < >>> gmo...@li...> wrote: >>> >>>> Hi all, >>>> >>>> I want to force labels on VCF tracks. I found this on a previous email: >>>> >>>> "style":{"labelScale": 0.01} >>>> However, I dont use trackList.json for my VCF configurations, I use >>>> tracks.conf. I tried setting it as style.labelScale = 0.01, but the labels >>>> are still not being drawn on the track for dense tracks. >>>> >>>> Thank you, >>>> -Hans >>>> >>>> >>>> _______________________________________________ >>>> Gmod-ajax mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>> >>> >> >> -- >> Hans Vasquez-Gross >> <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> >> PhD Candidate >> Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ >> Department of Plant Science >> University of California at Davis >> Email: hav...@uc... >> Skype: hansvg.ucd >> > > > -- > Hans Vasquez-Gross > <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> > PhD Candidate > Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ > Department of Plant Science > University of California at Davis > Email: hav...@uc... > Skype: hansvg.ucd > _______________________________________________ > 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: Hans Vasquez-G. <hav...@uc...> - 2021-03-29 18:03:32
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Also, is there a new setting to get html encoded in trask.conf or plugins to render? Here is an example using metadata. [ tracks.syn_a1hq ] storeClass = JBrowse/Store/SeqFeature/VCFTabix urlTemplate = syn/syn-wt_A-1.snpEff.highQ.vcf.gz category = VCF / Syn Ab #type = JBrowse/View/Track/CanvasVariants type = VariantEffectPlugin/View/Track/CanvasEffectVariants style.labelScale = 0.01 metadata.SNP-Colors = <span style='background-color:red'> </span> <span style='color:red'>(Red)</span> - SNPs with truncations<br><span style='background-color:purple'> </span> <span style='color:purple'>(Violet)</span> - amino acid changes<br><span style='background-color:green'> </span> <span style='color:green'>(Green)</span> - silent mutations<br><span style='background-color:blue'> </span> <span style='color:blue'>(Blue)</span> - outside gene regions key = A-1 SnpEff HQ Variants [image: Screen Shot 2021-03-29 at 11.01.38 AM.png] On Mon, Mar 29, 2021 at 9:02 AM Hans Vasquez-Gross < hav...@uc...> wrote: > Hi Colin, > > When we get our new webserver, I'll be setting it up so that we will have > a public instance. For now though, it requires connecting via university > VPN to load the website. > Here is a screenshot of the track config of the M-10 Variant > (non-labeled). > > [image: Screen Shot 2021-03-29 at 8.58.45 AM.png] > > > Best, > -Hans > > > > On Sun, Mar 28, 2021 at 10:57 PM Colin <col...@gm...> wrote: > >> The attribute style.labelScale=0.01 should be able to be used for forcing >> VCF labels to be drawn on dense tracks (e.g. >> https://jbrowse.org/docs/faq.html#my-track-doesn-t-display-the-gene-names-but-i-expected-it-to-why-not >> ) >> >> The value 0.01 corresponds to forcing labels to be drawn when you are >> zoomed in closer than about 100,000bp view window or so (e.g. >> 1000px/0.01pxPerBp=100,000bp) >> >> If you have an instance we can see that can be seen or any custom config, >> maybe that would help? >> >> -Colin >> >> On Fri, Mar 26, 2021 at 8:07 PM Hans Vasquez-Gross via Gmod-ajax < >> gmo...@li...> wrote: >> >>> Hi all, >>> >>> I want to force labels on VCF tracks. I found this on a previous email: >>> >>> "style":{"labelScale": 0.01} >>> However, I dont use trackList.json for my VCF configurations, I use >>> tracks.conf. I tried setting it as style.labelScale = 0.01, but the labels >>> are still not being drawn on the track for dense tracks. >>> >>> Thank you, >>> -Hans >>> >>> >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> > > -- > Hans Vasquez-Gross > <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> > PhD Candidate > Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ > Department of Plant Science > University of California at Davis > Email: hav...@uc... > Skype: hansvg.ucd > -- Hans Vasquez-Gross <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> PhD Candidate Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ Department of Plant Science University of California at Davis Email: hav...@uc... Skype: hansvg.ucd |
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From: Hans Vasquez-G. <hav...@uc...> - 2021-03-29 16:25:34
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Hi Colin, When we get our new webserver, I'll be setting it up so that we will have a public instance. For now though, it requires connecting via university VPN to load the website. Here is a screenshot of the track config of the M-10 Variant (non-labeled). [image: Screen Shot 2021-03-29 at 8.58.45 AM.png] Best, -Hans On Sun, Mar 28, 2021 at 10:57 PM Colin <col...@gm...> wrote: > The attribute style.labelScale=0.01 should be able to be used for forcing > VCF labels to be drawn on dense tracks (e.g. > https://jbrowse.org/docs/faq.html#my-track-doesn-t-display-the-gene-names-but-i-expected-it-to-why-not > ) > > The value 0.01 corresponds to forcing labels to be drawn when you are > zoomed in closer than about 100,000bp view window or so (e.g. > 1000px/0.01pxPerBp=100,000bp) > > If you have an instance we can see that can be seen or any custom config, > maybe that would help? > > -Colin > > On Fri, Mar 26, 2021 at 8:07 PM Hans Vasquez-Gross via Gmod-ajax < > gmo...@li...> wrote: > >> Hi all, >> >> I want to force labels on VCF tracks. I found this on a previous email: >> >> "style":{"labelScale": 0.01} >> However, I dont use trackList.json for my VCF configurations, I use >> tracks.conf. I tried setting it as style.labelScale = 0.01, but the labels >> are still not being drawn on the track for dense tracks. >> >> Thank you, >> -Hans >> >> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > -- Hans Vasquez-Gross <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> PhD Candidate Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ Department of Plant Science University of California at Davis Email: hav...@uc... Skype: hansvg.ucd |
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From: Colin <col...@gm...> - 2021-03-29 05:57:28
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The attribute style.labelScale=0.01 should be able to be used for forcing VCF labels to be drawn on dense tracks (e.g. https://jbrowse.org/docs/faq.html#my-track-doesn-t-display-the-gene-names-but-i-expected-it-to-why-not ) The value 0.01 corresponds to forcing labels to be drawn when you are zoomed in closer than about 100,000bp view window or so (e.g. 1000px/0.01pxPerBp=100,000bp) If you have an instance we can see that can be seen or any custom config, maybe that would help? -Colin On Fri, Mar 26, 2021 at 8:07 PM Hans Vasquez-Gross via Gmod-ajax < gmo...@li...> wrote: > Hi all, > > I want to force labels on VCF tracks. I found this on a previous email: > > "style":{"labelScale": 0.01} > However, I dont use trackList.json for my VCF configurations, I use > tracks.conf. I tried setting it as style.labelScale = 0.01, but the labels > are still not being drawn on the track for dense tracks. > > Thank you, > -Hans > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Hans Vasquez-G. <hav...@uc...> - 2021-03-27 00:07:21
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Hi all,
I want to force labels on VCF tracks. I found this on a previous email:
"style":{"labelScale": 0.01}
However, I dont use trackList.json for my VCF configurations, I use
tracks.conf. I tried setting it as style.labelScale = 0.01, but the labels
are still not being drawn on the track for dense tracks.
Thank you,
-Hans
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From: Colin <col...@gm...> - 2021-03-18 19:22:10
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I am maybe guessing, but maybe you are trying to view your rice GFF on the volvox (e.g. our demo's) FASTA assembly? The tracks may appear empty if the chromosome names from the GFF do not match the chromosome names from the FASTA (which would happen with an assembly mismatch e.g. volvox instead of rice being viewed here) -Colin On Thu, Mar 18, 2021 at 2:41 PM Scott Cain <sc...@sc...> wrote: > Hi anubhav, > > Can you tell us what you did to prepare the GFF data, and what the track > configuration looks like? If this site is available somewhere on the web > that we can get to, that would probably help too. > > Also, I know you are fairly new to jbrowse; let me suggest that you might > want to look at jbrowse 1, as it is more mature (I know I just steered you > away from GBrowse because it’s “too mature”). It all depends on what you > want the browser for. > > Scott > > > On Mar 18, 2021, at 10:29 AM, anubhav roy <anu...@gm...> > wrote: > > > > > > I have loaded Rice gff3 file but in GUI no genes or transcripts or any > information is shown.why? > > I want genes in my gff3 file to be shown in GUI. kindly help. > > screenshot is Attached. > > <jbrowse.png> > > _______________________________________________ > > Gmod-ajax mailing list > > Gmo...@li... > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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