Bowtie flags

[safisher]

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]

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 [email protected] 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.

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