From: Heewook L. <he...@um...> - 2012-02-27 18:18:08
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Rob, Actually i got this solved somehow.. instead of adding single track at a time with the flatfile script, I tured to biodb-to-json.pl. Anyhow, I have one more question: I have noticed all entries in gff when it's added to jbrowse via biodb-to-json.pl, start index always gets offset by 1. For example, if you have an entry in gff file and start and end is 1000 2000, when it's added on jbrowse, it will display as "start: 999, end: 2000. Why does this happen and are you aware of this? Thanks! On Mon, Feb 27, 2012 at 11:29 AM, Robert Buels <rb...@gm...> wrote: > Hi Heewook, > > Do you have the browser online anywhere that I can look at it? That would > help me diagnose what's going on. > > If you can't put it online, could you email me the > data/tracks/*/SNP/trackData.**json and data/trackInfo.js files so I can > look at them? > > Rob > > > > On 02/25/2012 01:44 AM, Heewook Lee wrote: > >> Thanks. It works great! >> >> I have one more question though. So now I have set up the jbrowse (using >> gbk2gff then biodb-to-json.pl <http://biodb-to-json.pl> with a config >> >> file similar to yeast configuration file you provide with the tarball) >> and now I want to add a track for displaying point mutations. I have >> already prepared the point mutations in a gff3 format so each point >> mutation in gff file is as : >> >> ecoliSNP90109010...ID=ecoli_**9010;Name=ecoli_9010;** >> Reference_Base=C;Consensus=C;**Modified_Call=T;snp_type=N-Syn >> >> >> since i have these point mutations in a separate file, I >> used bin/flatfile-to-json.pl <http://flatfile-to-json.pl> : >> >> $bin/flatfile-to-json.pl <http://flatfile-to-json.pl> --gff >> >> pointMutations.gff --tracklabel SNP --key SNP >> >> After this, when I refresh the jbrowse, I can see that new track, SNP >> has been added but the problem is it's not being rendered on the >> browser. When I zoom out enough I can see a histogram for the track but >> when i zoom in, I see nothing. What would I need to do to display SNPs >> correctly? Thanks! >> >> >> >> On Wed, Feb 15, 2012 at 12:14 PM, Robert Buels <rb...@gm... >> <mailto:rb...@gm...>> wrote: >> >> Hi Heewook, >> >> Bio::DB::SeqFeature::Store's behavior has changed slightly since >> that Current Protocols publication was written. In the >> NC_001133.gbk.gff, just remove the ##sequence-region line that the >> directions in the publication told you to alter, and the error >> should go away. Sorry for the inconvenience. >> >> Rob >> >> >> >> On 02/10/2012 01:32 PM, Heewook Lee wrote: >> >> -------------------- EXCEPTION -------------------- >> MSG: segment() called in a scalar context but multiple features >> match. >> Either call in a list context or narrow your search using the >> -types or >> -class arguments >> >> STACK Bio::DB::SeqFeature::Store::__**segment >> /usr/local/share/perl5/Bio/DB/**__SeqFeature/Store.pm:1359 >> STACK toplevel bin/prepare-refseqs.pl:156 >> <http://prepare-refseqs.pl:156**> <http://prepare-refseqs.pl:** >> 156__> >> >> ------------------------------**__------------- >> >> >> Any idea how I can get around this? Thanks >> >> >> > |