PeakSeq mappability map

[Wonko]

Hi everyone,
I am trying to generate a mappability map of hg19 Chr21. When running

python compile.py 76

I get the error

/bin/sh: chr2hash: not found
/bin/sh: OligoFindPLFFile: not found
/bin/sh: mergeOligoCounts: not found

The executables are in a folder I generated for PeakSeq and added to /etc/environment. What do I have to change?

Thanks,
wonko

[frankyue50]

you need to add it to your PATH, for example .bash_profile

[AL_B]

Mappability Map missing chromosomes

Hi,
When I create Mappability map file (I am using the code given in Gerstein Lab http://archive.gersteinlab.org/proj/...lity_Map/Code/ ), in some cases, there are chromosomes that are missing in the output mappability map file. Does any one knows why? All the needed .fa files are in the directory of mappability map.

Thanks in advance