Hi.
As the post title says, when I run this command: python -m HTSeq.scripts.count -f bam -s no -i ID -t exon -r name ./name_sorted.bam ./Ppersica_298_v2.1.gene_exons.gff3 > ./Counts
the output file size are always 10mb. I have done this at least 5 times in a row, with the same command on different Prunus Persica bam files (output from Tophat2, RNA-Seq data) which were name sorted using samtools.
It's weird that all the files has the same size, like HTSeq-count has a limit size for the output, or maybe my command is wrong?
Exactly. Every feature in your GTF file will be present in the output of htseq count. But for a lot of the exons in there, the count will be 0.
So my file sizes are fine. Thanks a lot for the quick answer.