How To Use Bfast To Align Color Space Reads

Question

[Raygozak]

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.

Answer 1

[Istvan Albert]

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