I am doing the bacterial NGS data analysis and i ran the Htseq after Bowtie on my data. Can some on explain me the meaning of too low aQual numbers in result. The other thing that since Bowtie has mapped alreday with the bactreial genome then why Htseq count still showing a high number of reads which are not aligned.
aQual is supposed to mean the alignments mapping quality score (aka, the MAPQ).
You can instruct bowtie to include unaligned reads in its output, in which case you'll see them mentioned in the htseq-count output. Additionally, many reads will map to intergenic regions, which may also be what you're seeing.
Many thanks for your reply. How can I get counts from intergenic region in htseq for ex if I want to see the reads coming from 5' and 3" UTRs. I was wondering why the total read aligned don't match with the numbers that I obtained after adding up all the the reads counted by ht-seq (CDS+ncRNA+tRNA+rRNA).