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