Multi mapped reads

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1

Hello,
I am new in galaxy and i want to know how to get the multi mapped reads in different file

2

Welcome, @ATIKAKO_KOSSIVI

This topic at the Biostars forum has a good explanation for this → How to filter/view reads mapped to multiple locations using samtools or pysam

So, filter your BAM file first, then if you want the associated fastq reads in a separate file extract them after.

Filtering a BAM file

Try a search in the tool panel with the keywords: filter bam. This is one of the options:

  • Filter BAM is the Bamtools version of this operation, same as described in that post above (link at UseGalaxy.org)

Exact Fastq from a BAM

Once you have the BAM filtered, you can then use a tool to extract the fastq reads.

Hopefully this helps, and you can ask more questions. :slight_smile: Searching the panel with keywords at a UseGalaxy server is a really good way to find these standard conversion/filtering tools. And you can ask more questions if you can’t find something.