Question: Obtaining Quality score of the mapped sequences - BBMap
2
gravatar for madhu.9124
2.5 years ago by
madhu.912440
madhu.912440 wrote:

Hi,

I am new to BBMap, so I kindly request to help me to find the **quality score of the mapped sequences. I also want to increase the quality score of the mapped sequence.

Thanks Madhu

alignment • 2.3k views
ADD COMMENTlink modified 9 months ago by madzayasodara0 • written 2.5 years ago by madhu.912440

Are you referring to alignment scores (MAPQ values, column 5)? Those are in the SAM/BAM files. Otherwise this question is missing what it is you are looking for.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax75k

thanks, I want the MAPQ value. Any idea of the command to get the MAPQ value using SAMtool.

ADD REPLYlink written 2.5 years ago by madhu.912440
1

What will you do with standalone MAPQ values? You could do something like samtools view test.bam | awk -F "\t" '{print $5}' OR awk -F "\t" '{print $5}' your_file.sam

ADD REPLYlink modified 22 months ago • written 2.5 years ago by genomax75k

thanks a lot, I just want to retrieve the value and increase the value to test the BBMap application.

ADD REPLYlink written 2.5 years ago by madhu.912440

missing ' after

awk -F "\t" '{print $5}

ADD REPLYlink written 22 months ago by arup1.9k

Added to post above and here awk -F "\t" '{print $5}' your_file.sam

ADD REPLYlink written 22 months ago by genomax75k

You guys sure there's not a sam/bamtools cmd that straight up does this? I did my alignment using BWA. I could loop through my 23 whole-genome bam files doing this, but It's gonna be real slow...

ADD REPLYlink modified 9 months ago • written 9 months ago by madzayasodara0
1

the original question is somewhat undefined. What is the purpose of extracting the mapping quality?

If one wanted to filter alignment by a minimal score this can be done with

samtools view -q 10 myfile.bam

where

 -q INT   only include reads with mapping quality >= INT [0]
ADD REPLYlink modified 9 months ago • written 9 months ago by Istvan Albert ♦♦ 81k
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