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Old 11-27-2013, 08:44 AM   #1
antoza
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Location: France

Join Date: Aug 2013
Posts: 18
Default problem GFF3 file display its attribute tag in IGV

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
Attached Images
File Type: png igv_snapshot2.png (33.9 KB, 9 views)
Attached Files
File Type: txt example_GFF3.txt (542 Bytes, 0 views)

Last edited by antoza; 11-27-2013 at 08:51 AM.
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