Multitasking and Rbwa
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@d12fee30
Last seen 16 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 • 833 views
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@james-w-macdonald-5106
Last seen 9 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.

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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)
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