Custom mappability file

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Hello,

I have seen that a similar question has already been asked but apparently it 
did not receive any answer. I'll try to submit it again:
How to generate custom mappability files?
Thanks in advance.

Original issue reported on code.google.com by Sara.Cas...@gmail.com on 27 May 2013 at 1:22

[GoogleCodeExporter]

Split your genome reference fasta into separate chromosomes with BioPython and 
put them in a directory, making sure that they end in '.fa' (as explained in 
http://www.biostars.org/p/14092/) :

from Bio import SeqIO
seqs = SeqIO.parse(open(fasta_file), format='fasta')
for seq in seqs:
   name = seq.id+'.fasta'
   SeqIO.write(seq, open(name, 'w'), format='fa')

Then download Mappability map code from Gerstein's lab :
http://archive.gersteinlab.org/proj/PeakSeq/Mappability_Map/Code/

Make the three executables chr2hash, oligoFindPLFFile, mergeOligoCounts, using 
the Makefile. Make sure they are in your PATH.

Put compile.py in your PYTONPATH or copy it in the .fa directory and in this 
directory containing the .fa files, do: 

$ python compile.py K

where K is the length of your reads.

At the end of the process, you can only keep *b.out files and map.list and 
temp.wig.

Hope it helps,
Fabien Pichon

Original comment by fabien.p...@gmail.com on 27 Nov 2013 at 9:43