Getting expression for miRNAseq data - 0 counts?

[lbeltrame]

Hello everyone,

thanks to the advice provided in the other thread (for reference: http://seqanswers.com/forums/showthread.php?t=17282) I managed to get reasonable alignment percentages. Now I'm moving to the next step, calculating expression.

At the moment however, I can't seem to get any count out, using htseq-count from the Python HTSeq package.

For GFF/GTF, I downloaded the GFF file from mirBase, and invoked htseq-count as follows:

htseq-count -q -i ID -t miRNA test.sam miRNA_hsa.gff

However, all features come out as a net count of 0. I'm pretty sure I made one (or more) mistake, but I don't have a clue on where to look for... any suggestions?

[lbeltrame]

I solved the issue myself, so I'm leaving this for posterity. Basically the GFF file from mirBase is not that good. I retrieved the relevant table from the UCSC Genome Browser and I finally got my counts correctly.

[Palgrave]

Hi,

Could you specify which file you downloaded and if you edited it some way and how you ran the script? Did you use sam from bowtie output as your input?

Best