Mapping quality plot of BAM file

Question: Mapping quality plot of BAM file

22 months ago by

vebaev • 130

vebaev • 130 wrote:

I'm interested in a specific genome region, is there a way/tool to make trackster track/plot/histogram/ of mapping quality from BAM?

plot mapping quality • 3.0k views

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modified 22 months ago by y.hoogstrate • 460 • written 22 months ago by vebaev • 130

22 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Trackster does not display this data, but IGV does.

Other options include running one of Galaxy's plotting tools on the MAPQ column directly to generate statistics/graphics.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k

22 months ago by

y.hoogstrate • 460

Netherlands

y.hoogstrate • 460 wrote:

Hi there,

You can use samtools view (in Galaxy as the following tool Filter SAM or BAM , output SAM or BAM files on FLAG MAPQ RG LN or by region) to subselect the region.

With that alignment you can go back to FASTQ and :

Then dump the BAM to FASTQ (FastqToSam convert Fastq data into unaligned BAM).
And then proceed with FastQC to get a general report of Quality.

Or proceed with the BAM file and use tools that estimate base-quality within BAM files. I don't know this by heart, but I would expect deepTools or Picard tools might have something like this.

Good luck,

Youri

ADD COMMENT • link written 22 months ago by y.hoogstrate • 460

Hi Youri, First part is great for subsetting by region! For the second part, this is to generate a report of the fastq quality scores, correct? I think the user wanted the mapping quality - but they can correct us :) Thanks, Jen

ADD REPLY • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k

Oops, that should be possible too. Convert to SAM and exclude the header, use cut in Galaxy to pick column 5 (https://samtools.github.io/hts-specs/SAMv1.pdf, sec 1.4) and visualize this in Galaxy Charts.

ADD REPLY • link modified 22 months ago • written 22 months ago by y.hoogstrate • 460

Thanks Yuori for adding in the details! Jen

ADD REPLY • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k

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