Finding Mappability With Peakseq

Question

[KCC]

There are few similar questions to this one, but not very much detail.

I downloaded the Mappability code from here: http://archive.gersteinlab.org/proj/PeakSeq/Mappability_Map/Code/

Based on the README, I made the three executables: chr2hash, oligoFindPLFFile and mergeOligoCounts; I put them in the same directory as my chromosomes.

Then I tried: python compile.py 30

This generated many *.out files.

By process of elimination I haven't used map.py or CountMap.py yet so I assume they need to be used next. The README cryptically says:

"Then, use CountMap.py in the usual way to access the data."

What do I do next? How do I generate the mappability files?

Answer 1

[Vikas Bansal]

The next step with CountMap.py is described in pipeline here. It says-

Run the counter:
/bin/countMaps.py [-c <count dir>] [-o <output dir>] [-w <window size>] [-h]
-c directory where you did the count
-o directory where you want the mappability file to be (if not given, ~/solexa/mappability)
-w window size (if not given, 1,000,000)
-h help

Answer 2

[Casey Bergman]

The only usable & available "mappability" software that I have found is GEM. Note, however, that GEM computes "uniqueness" (an intrinsic property of your reference genome) not "mappability" (a combined property of your reference genome, sequence data and mapping software).

[chhylp123]

Hi, recently, I have a problem about GEM. When I want build index for human using GEM, it reported

Creating sequence and location files...
Fatal error: exception
Failure("Command 'echo "-------gem-indexer_fasta2meta+cont" > human_g1k_v37.fasta.log && gem-indexer_fasta2meta+cont -i human_g1k_v37.fasta -c dna --filter-function iupac-dna --strip-unknown-bases-threshold 50 --complement-size-threshold 2000000000 --comp.

The command I used is

./gem-indexer -i /devdata/chhy/masai/bin/human_g1k_v37.fasta -o hum.index -T 4

Could you help me to solve this problem?

Thanks!

[7lagrange]

you should add the program into the PATH

[hongen.hugo.xu]

this solved the problem same with chhylp123. Thanks