Question: what is thye meaning of too low aQual in Htseq
0
gravatar for sandy.mbt
16 months ago by
sandy.mbt0
sandy.mbt0 wrote:

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.

rna-seq • 534 views
ADD COMMENTlink modified 15 months ago • written 16 months ago by sandy.mbt0
1
gravatar for Devon Ryan
15 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

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.

ADD COMMENTlink written 15 months ago by Devon Ryan1.9k
0
gravatar for sandy.mbt
15 months ago by
sandy.mbt0
sandy.mbt0 wrote:

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).

ADD COMMENTlink written 15 months ago by sandy.mbt0

There's no reason to restrict htseq-count to CDS. Intergenic counts are the no_feature number. There will always be a fair number of those, mostly from background transcriptional noise.

ADD REPLYlink written 15 months ago by Devon Ryan1.9k
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