Open GoogleCodeExporter opened 8 years ago
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
Original issue reported on code.google.com by
Sara.Cas...@gmail.com
on 27 May 2013 at 1:22