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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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Bowtie flags #157

Open safisher opened 11 years ago

safisher commented 11 years ago

I have some old Illumina files to align. I believe they require the bowtie flag "--solexa1.3-quals". Can I set this flag through rum_runner? I didn't see anything in the docs about sending arguments to bowtie.

Thanks.

mdelaurentis commented 11 years ago

This is not an option at this time, though it would be pretty easy to add. I'll just add a '--bowtie-flags' option that takes a string of arbitrary parameters to pass into Bowtie.

In the meantime, you can modify the lib/RUM/Bowtie.pm file locally to add those flags, if you need to.

On Thu, Dec 13, 2012 at 3:52 PM, safisher notifications@github.com wrote:

I have some old Illumina files to align. I believe they require the bowtie flag "--solexa1.3-quals". Can I set this flag through rum_runner? I didn't see anything in the docs about sending arguments to bowtie.

Thanks.

— Reply to this email directly or view it on GitHubhttps://github.com/PGFI/rum/issues/157.