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Thread | Thread Starter | Forum | Replies | Last Post |
Problem with Gbrowse 1.7 old version: it does not recognize the gff3 file well | sunfuhui | General | 0 | 08-06-2012 11:41 AM |
GFF3 display in IGV | Alexander Tchourbanov | Bioinformatics | 2 | 02-13-2012 12:31 AM |
Problems with display in IGV | keo | General | 4 | 02-02-2012 07:27 AM |
missing reads in IGV display | cswarth | Bioinformatics | 2 | 06-28-2011 09:30 AM |
IGV display of coverage | john_mu | Bioinformatics | 2 | 06-05-2010 11:40 PM |
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#1 |
Member
Location: France Join Date: Aug 2013
Posts: 18
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Hi folks,
I would like to upload a GFF3 annotation file in the IGV 2.3 viewer along with a fasta file correspond to a genome. Everything is displayed OK (all the genome contigs are properly display the GFF3 features). My GFF3 file is as the below example corresponding to gene00001 (also found it attached). velvet_01_NODE_275_length_47636_cov_8.196805 ALN gene 807 1259 2 + . ID=gene00001;Name=velvet_000040_1;isoforms=1 velvet_01_NODE_275_length_47636_cov_8.196805 ALN mRNA 807 1259 625 + . ID=mRNA00001;Parent=gene00001;Name=velvet_000040_1 velvet_01_NODE_275_length_47636_cov_8.196805 ALN exon 807 995 383 + . ID=exon00001;Parent=mRNA00001;Name=velvet_000040_1;Target=CH063_02577T0 1 189 + velvet_01_NODE_275_length_47636_cov_8.196805 ALN exon 1125 1259 275 + . ID=exon00002;Parent=mRNA00001;Name=velvet_000040_1;Target=CH063_02577T0 190 324 + The problem lies on the fact that I would like to being displaying in IGV the “Target” tag values of attributes section (“CH063_02577T0” in my case and for this gene), Until know when I insert the GFF3 file what was being displaying is mRNA00001 and gene00001 (please see the attached snapshot). So what I would like to being showing is mRNACH063_02577T0 and geneCH063_02577T0. Please try to help me if it feasible; I am too frustrated with this ![]() Last edited by antoza; 11-27-2013 at 08:51 AM. |
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