I'm interested in a specific genome region, is there a way/tool to make trackster track/plot/histogram/ of mapping quality from BAM?
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
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.
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
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.
Thanks Yuori for adding in the details! Jen