Question: Feeding HTSeq-Count with a GFF taken from GDR Database
gravatar for cr.balladares.m
3.7 years ago by
cr.balladares.m10 wrote:


Im trying to feed HTSeq-Count with this GFF taken from the GDR Database. I'm using this command line:

python -m HTSeq.scripts.count -f bam -s no -i ID -t gene -r name name_sorted.bam Prunus_persica_v2.0.a1.gene.gff3 Output.txt

The GFF looks like:

Pp01 JGI gene 40340 51496 0 + 0 ID=Prupe.1G000100_v2.0.a1;Name=Prupe.1G000100;ancestorIdentifier=ppa023343m.g.v1.0 Pp01 JGI mRNA 40340 51496 0 + 0 ID=Prupe.1G000100.2_v2.0.a1;Name=Prupe.1G000100.2;longest=0;Parent=Prupe.1G000100_v2.0.a1 Pp01 JGI five_prime_UTR 40340 40475 0 + 0 ID=Prupe.1G000100.2_v2.0.a1.five_prime_UTR.1;Parent=Prupe.1G000100.2_v2.0.a1 Pp01 JGI CDS 40476 40616 0 + 0 ID=Prupe.1G000100.2_v2.0.a1.CDS.1;Parent=Prupe.1G000100.2_v2.0.a1 Pp01 JGI CDS 40721 40830 0 + 0 ID=Prupe.1G000100.2_v2.0.a1.CDS.2;Parent=Prupe.1G000100.2_v2.0.a1

It's from a RNA-Seq experiment. I don't exactly know how HTseq-Count works and as far as I know it uses GFF from Ensembl, so I don't know if my options are right according to the GFF.

Thanks in advance.

rna-seq htseq-count gff • 1.2k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by cr.balladares.m10

Are you having any problems? Any error messages? Any messages at all? I am not sure if you want an opinion before you begin, or if you are having problems which you didn't report.

ADD REPLYlink written 3.7 years ago by h.mon29k

I want both, I want an opinion and I think Im having problems in my results. I used the output in edgeR, Limma and DESeq and comparing with the gene_exp.diff file (from cufflinks) I got too little DE genes, so I thought it was some problem with the counts.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by cr.balladares.m10
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