Solanum lycopersicum gff htseq-count

Hi all. Dont know how to solve this, so here it goes. trying to do an rna-seq analysis on solanum lycopersicum. I am at the step of htseq-count so i got the gff from this website: https://solgenomics.net/organism/Solanum_lycopersicum/genome/ ->> ITAG4.0. I used to do rna-seqs on humans so in the hg19.gtf file there were "gene_id" therefore i could use the option " -i gene_id " when executing htseq-count command. On this gff (a portion of the gff file):

SL4.0ch00   maker_ITAG  gene    417592  418482  .   +   .   ID=gene:Solyc00g500004.1;Alias=Solyc00g500004;Name=Solyc00g500004.1;length=890
SL4.0ch00   maker_ITAG  mRNA    417592  418482  .   +   .   ID=mRNA:Solyc00g500004.1.1;Parent=gene:Solyc00g500004.1;Name=Solyc00g500004.1.1;Note=Unknown protein;_AED=0.47;_QI=0|0|0.5|1|0|0|2|524|98;_eAED=0.56
SL4.0ch00   maker_ITAG  exon    417592  417723  .   +   .   ID=exon:Solyc00g500004.1.1.1;Parent=mRNA:Solyc00g500004.1.1
SL4.0ch00   maker_ITAG  CDS 417592  417723  .   +   0   ID=CDS:Solyc00g500004.1.1.1;Parent=mRNA:Solyc00g500004.1.1
SL4.0ch00   maker_ITAG  CDS 417794  417958  .   +   0   ID=CDS:Solyc00g500004.1.1.2;Parent=mRNA:Solyc00g500004.1.1
SL4.0ch00   maker_ITAG  exon    417794  418482  .   +   .   ID=exon:Solyc00g500004.1.1.2;Parent=mRNA:Solyc00g500004.1.1
SL4.0ch00   maker_ITAG  three_prime_UTR 417959  418482  .   +   .   ID=three_prime_UTR:Solyc00g500004.1.1.0;Parent=mRNA:Solyc00g500004.1.1

Is there an option on htseq-count i could use for the genes? Or is there a way to convert this gff file to the one like the hg19.gtf - image below

hg19.gtf

rna-seq

• 1,524 views • link

written 5.7 years ago by dimitrischat

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image or the HTML embed code, not the link to the webpage that has the image embedded (which is what you have used here)

• 0 views • link

written 5.7 years ago by Ram

0 answers

No answers yet.