Problems Running The Peakseq Mappability Code

Question

[Arturo_M]

Hi Im kind of new in linux and I am trying to create a Mappability File using the executables and instructions that are part of peakseq that are here http://archive.gersteinlab.org/proj/PeakSeq/Mappability_Map/Code/ Finally when I do python compile.py I get this

/bin/sh: 1: chr2hash: not found                     
/bin/sh: 1: oligoFindPLFFile: not found           
/bin/sh: 1: mergeOligoCounts: not found

I know this has to do with put them in my PATH but I dont understand what does that mean. Could someone please explain that to me and what should I do to solve this problem?

Thanks I really appreciate your time

Answer 1

[Ketil]

You can set the PATH variable (which tells the shell where to look for executables) with:

export PATH=$PATH:/path/to/executables/

If you don't know where chr2hash et al lives, you can try to find out with 'find' or 'locate'.

(If you run a Unix system, shouldn't you have somebody around that can help you with the basics?)

Answer 2

[Arturo_M]

Thanks I tried what you kindly answered, but I got the same message for the three executables...do you have any idea why isnt it working?

Again thank you

Answer 3

[Arturo_M]

Forget it I got that. Thank you for your help. Now I have a different issue. Once all files were produced using python compile.py, what are the files that CountMap.py takes as input... I tried all the different ones for a chromosome but I get this " SyntaxError: Non-ASCII character '\xac' " Do I need to process this files before using CountMap.py? And if thats the case which program should I use?

Thanks again