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Old 01-29-2014, 12:04 AM   #1
foolishbrat
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Location: South East Asia

Join Date: Nov 2008
Posts: 44
Default Meaning of Negative Alignment Score in BOWTIE2 output

I have a mIRNA seq data in which I aligned it to whole genome UCSC hg19.
For that I use bowtie2 with the following parameter:

Code:
bowtie2 -x myindex -U my_mirna_seq.fastq --n-ceil L,0,0 -k 1 -N 1  -S mydata.sam
However in the SAM output I notice the alignment score is negative:


Code:
$cut -f12  mydata.sam | grep AS | sort -u | tail 
AS:i:-29
AS:i:-3
AS:i:-30
AS:i:-4
AS:i:-5
AS:i:-6
AS:i:-7
AS:i:-8
AS:i:-9
AS:i:0
What does it mean to have -ve AS value?
How should I deal with it?

And also the MAPQ score is 255 for all the alignments, no others.
Is that normal?

Last edited by foolishbrat; 01-29-2014 at 12:13 AM.
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