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:
However in the SAM output I notice the alignment score is negative:
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?
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
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
How should I deal with it?
And also the MAPQ score is 255 for all the alignments, no others.
Is that normal?
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