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How To Use Bfast To Align Color Space Reads

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.

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updated by Istvan Albert Istvan Albert • written by Raygozak Raygozak

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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

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written by Istvan Albert Istvan Albert

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