HTSeq-count output files sizes are always 10mb

Question

[cr.balladares.m]

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?

Answer 1

[karl.stamm]

If you're counting reads at sites, the output file will always be a list of the same length.

The input data would have to be an order of magnitude different in total reads to have any impact on the number of characters in the counts column.

[WouterDeCoster]

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.

[cr.balladares.m]

So my file sizes are fine. Thanks a lot for the quick answer.