Hi all,

I'm getting counts on __too_low_aQual from htseq-count even when I set the minaqual to zero (--a=0).

no_feature 33468765ambiguous 135603 __too_low_aQual 5342122 __not_aligned 432861 __alignment_not_unique 0

The number of alignments with MAPQ equal to zero on bam file is less than that reported by htseq-count.

samtools view 1.bam | awk 'FNR>=1{for(i=1;i<=NF;i++){ if($5==0){print ; next; } }}' | wc -l 932433

And there is no alignment with MAPQ less than zero...

Any guesses of what's happening?

Thanks!