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4 hours ago by

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: 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 ( freeimage.host/i/FEvxBs )

enter image description here

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modified 3 hours ago

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4 hours ago
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dimitrischat120



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