I'm using STAR to 2-pass alignment and htseq-count to output gene count table. But my htseq-count result table is a bit strange, like follow:
__no_feature 5802774 __ambiguous 4365152 __too_low_aQual 0 __not_aligned 0 __alignment_not_unique 0
all alignments are in no feature or ambiguous couters. Why does this happen. My code is:
htseq-count -s no Aligned.out.sorted.sam gencode.v28.annotation.gtf > samp.htseq-count.tab
Any one has got same problem?