Question: how to extract mapped reads from output of BWA-MEM to a separate file?
gravatar for jerrry113
2.5 years ago by
jerrry1130 wrote:

Hello all,

By default, BWA-MEM on the main galaxy server does not seem to give an option to write the mapped or unmapped reads in an alignment run to its own separate file. Is there a utility available on Galaxy that I can use to parse through the BAM output for just the reads that aligned? Thanks!

  • Jerry
mapping bwa bwa-mem galaxy samtools • 1.7k views
ADD COMMENTlink modified 2.4 years ago by y.hoogstrate460 • written 2.5 years ago by jerrry1130
gravatar for y.hoogstrate
2.4 years ago by
y.hoogstrate460 wrote:

Hello Jerry,

Together with the bitwise flags given in this document: and the tool "Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region (Galaxy Version 1.1.2)" you should be able to solve it. Good luck!


ADD COMMENTlink written 2.4 years ago by y.hoogstrate460
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