I have some chip-seq data and I want to do some peak calling. To do peak calling with ZINBA, peakseq, MOSAiCS I need to have mappability data.
This data is given for hg19 ( http://www.bios.unc.edu/~nrashid/map50_hg19.tgz from this page http://code.google.com/p/zinba/wiki/UsingZINBA) however, the chip-seq data I use thus far have been aligned to 1000 genome's version of hg19 ( ftp://ftp.sanger.ac.uk/pub/1000genomes/tk2/main_project_reference/) and I do not wish to realign all the data I have (previously I have been using MACS, I want to see results from other peak callers)
I have tried to run ZINBA using hg19 mappability files but I get a segfault pretty early on. Thus, I am trying to generate these mappability files: I get the feeling that these files are unique to whatever you used as reference (so hg19 with chr1-22+x,y mappability files would not be interchangeable with chr1-22+x,y,M)
I was wondering if someone could shed some insight into what these mappability files are and if they are interchangeable (because if they are then I would only have to generate M+supercontigs for 1000 genome's version of hg19 and use chr1-22 from the available hg19).
Additionally, I was wondering if this was the right program to generate these files: http://archive.gersteinlab.org/proj/PeakSeq/Mappability_Map/Code/