Thanks I was able to figure out.
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convert GFF to GTF?
I am trying to convert gff to gtf. I got this from JGI.
scaffold_1 JGI exon 6764 7298 . - . name "estExt_Genewise1.C_1_t10003"; transcriptId 510443
scaffold_1 JGI CDS 6997 7298 . - 2 name "estExt_Genewise1.C_1_t10003"; proteinId 510305; exonNumber 3
scaffold_1 JGI stop_codon 6997 6999 . - 0 name "estExt_Genewise1.C_1_t10003"
I used:
gffread genes.gff -T -o genes.gtf
genes.gtf file is like this:
scaffold_1 JGI exon 1131 1262 . + . transcript_id "name";
scaffold_1 JGI exon 2725 3036 . + . transcript_id "name";
scaffold_1 JGI exon 5439 5651 . + . transcript_id "name";
scaffold_1 JGI exon 19128 19223 . + . transcript_id "name";
scaffold_1 JGI exon 23365 23825 . + . transcript_id "name";
Why there is "name" instead of actual ID?
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2 answers
I guess gffread doesn't like the gff flavour you are giving as input. The problem comes from the attributes of the 9th column:
in gff3 :
name="e_gw1.5.2.1"; transcript_id=335995
in gff2.5 :
name="e_gw1.5.2.1" transcript_id=335995
in gff2/gtf/gtf2.2 :
name "e_gw1.5.2.1"; transcript_id 335995
in gff? from another source i have seen:
name "e_gw1.5.2.1" transcript_id 335995
in gff1:
ID1
So you have to first modify your file to have a gff3 or gff2.5 flavor.
But it will not be needed, what you have at the beginning seems already be the format you want !! You juste have to keep the exon lines and modify transcriptId per transcript_id.
Thanks. I was able to figure out.
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