I am using htseq-count. I want to count also the ambiguous so I am using ‘--nonunique all’, I cannot understand why when using --nonunique all, I got the same number in ‘__too_low_aQual’ and in ‘__alignment_not_unique’.
Does the reads in ‘__too_low_aQual’ also counts for genes?
My commands for using or un-using ‘--nonunique all’:
htseq-count --mode=union --nonunique all --stranded=yes --minaqual=10 --type='exon' file.sam gencode.v32.primary_assembly.annotation_with_CMV.gtf > output_file
__no_feature 1996365
__ambiguous 78263
__too_low_aQual 1990338
__not_aligned 0
__alignment_not_unique 1990338
Sum counts 2139001
htseq-count --mode=union --nonunique all --stranded=yes --minaqual=10 --type='exon' file.sam gencode.v32.primary_assembly.annotation.gtf > output_file
__no_feature 1996365
__ambiguous 78263
__too_low_aQual 0
__not_aligned 0
__alignment_not_unique 1990338
Sum counts 1971151
