Question: Mapping quality plot of BAM file
0
gravatar for vebaev
12 months ago by
vebaev130
Bulgaria
vebaev130 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 • 1.4k views
ADD COMMENTlink modified 12 months ago by y.hoogstrate460 • written 12 months ago by vebaev130
1
gravatar for Jennifer Hillman Jackson
12 months ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 12 months ago by Jennifer Hillman Jackson23k
0
gravatar for y.hoogstrate
12 months ago by
y.hoogstrate460
Netherlands
y.hoogstrate460 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 COMMENTlink written 12 months ago by y.hoogstrate460

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 REPLYlink written 12 months ago by Jennifer Hillman Jackson23k
1

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 REPLYlink modified 12 months ago • written 12 months ago by y.hoogstrate460
1

Thanks Yuori for adding in the details! Jen

ADD REPLYlink written 12 months ago by Jennifer Hillman Jackson23k
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