Question

Multitasking and Rbwa

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Franck RICHARD • 0

@d12fee30

Last seen 17 months ago

Spain

Hello !

How can I activate multitasking with Rbwa when creating a reference index or alignment?

The "-t" parameter doesn't work...

Thank you!

Rbwa Alignment • 860 views

ADD COMMENT • link written 18 months ago by Franck RICHARD • 0

score 0 · Answer 1 · 2023-05-30

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 10 hours ago

United States

There is no -t argument for bwa_build_index, so if that's what you are basing your question on, that's the reason. There is a -t argument for bwa_aln, and it looks like Rbwa just calls bwa_aln directly, so it should work.

ADD COMMENT • link 18 months ago James W. MacDonald 67k

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Indeed, one can pass additional arguments to the bwa_aln function in Rbwa:

 bwa_aln(type="single", 
     index_prefix=index_prefix, 
     fastq_files=fastq_files,
     sai_files=sai_files,
     t=3)

ADD REPLY • link 18 months ago Jean-Philippe Fortin • 0