I have aligned my RNA sequences against human genome GRCh38.p13. Then I am using htseq-count to count the reads per gene. The below is the command I am using:
htseq-count ./sorted-bams/f.bam ./gencode.v41.chr_patch_hapl_scaff.annotation.gff3.gz > ./htseq/f.txt
In the output file, I got :
__no_feature 2280226 __ambiguous 244 __too_low_aQual 3761161 __not_aligned 34990259 __alignment_not_unique 0
Are these numbers reasonable?