4 months ago by
Use a combination of Samtools. Picard, and Text Manipulations tools.
Filter the SAM/BAM for aligned reads, then convert BAM to SAM (if needed, the goal is to exclude the header. From there you can pull out the sequence identifiers and sort them uniquely or count up hits per read, etc. If you want the reads in fastq format, BAM/SAM to fastq can be used. Once you have a process worked out, there is an option to extract a workflow and run all the tools later in batch mode (will behave like a custom tool).
Please note that workflows are problematic today but this should be cleared up quickly and does not impact directly running tools. Details here: https://biostar.usegalaxy.org/p/28818/#28823
Galaxy tutorials: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team