Question: How To Use Bfast To Align Color Space Reads
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gravatar for Raygozak
6.1 years ago by
Raygozak1.2k
State College, PA, Penn State
Raygozak1.2k wrote:

Hi, i'm new to Bfast and i'm trying to index a genome into colorspace, since bowtie2 doesn't support color space i went to Bfast, but can't find any detailed information on what should i actually input on the -m (mask) option, or what does it actually mean and how can i decide what's the best for my data.

solid • 2.3k views
ADD COMMENTlink modified 6.1 years ago by Istvan Albert ♦♦ 78k • written 6.1 years ago by Raygozak1.2k
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gravatar for Istvan Albert
6.1 years ago by
Istvan Albert ♦♦ 78k
University Park, USA
Istvan Albert ♦♦ 78k wrote:

The documentation for BFAST does not seem to be linked from their main site (quite strange!) but I found a manual see below, look at the section called 5.6 Color Space Alignment:

http://helix.nih.gov/Applications/bfast-book.pdf

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Istvan Albert ♦♦ 78k
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