miRNA cleanup

[ewels]

Hi @s-andrews and @FelixKrueger,

Any comments on these changes?

• Made a copy of sra_bowtie_miRNA.config for use with FastQ files
• Removed adapter=ATGGAATTCTCG from the TrimGalore step as no longer needed
• Forced both pipelines to use bowtie1 instead of choosing.
  • The bowtie2 module doesn't recognise the mirna parameter
  • Renamed pipelines to reflect this change.

Does this all look ok? Are these pipelines still good as the standard way to process miRNA data?

Cheers,

Phil

[s-andrews]

I think that's fine. We don't tend to use those pipelines much - they were set up when you wanted to map reads to mirBase samples rather than to a genome. They set somewhat lax mapping paramters and allow multiple mapping which is what you want when you're mapping to known miRNAs but gets confusing it you use them on a genome.

Simon.

[ewels]

Ok thanks - should I change the help text then? It currently says:

The pipeline is designed to run against miRNA database libraries, but can also be used against genomic libraries.

Maybe I could make it more obvious that it's for mirBase only?

[s-andrews]

It can be used on genomic libraries as long as you understand what you're getting out of it so it's not an unreasonable description. It's just not what we'd use on genomic searches by default.

[ewels]

Ok cool, I'll merge then 👍 Thanks!