Hello, I would like to use F-seq program but I wonder if there is a way to create your own bff files ( the background files)? I could not find anything useful in the software site.
Thank you for your time
Someone I work with was able to obtain bffbuilder from the Furey Lab. Have you contacted them? I don't why the program is not available from the Fseq download site!
The basic pipeline is to download the CGR Mappability data appropriate for the sequence reads you are using (e.g. 75 mers), example. The file first has to be converted from bedGraph to WIG (my contact was provided with a converter to do this). Then run bffbuilder. It failed for me at that point, but apparently you need to work on one chromosome at a time.
Update on how you get on. If more people ask for access to the program they may release it on the website. I don't feel that I can just provide the software as it seems to be restricted at the moment...
For future reference, this is all available on the Furey lab webpage now: http://fureylab.web.unc.edu/software/fseq/
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Thank you for your answer I will contact Furey lab.