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Old 08-24-2013, 11:41 AM   #1
Junior Member
Location: israel

Join Date: Aug 2013
Posts: 5
Default Creating Mappability Map file

I have downloaded the mappability map code, from:
I followed the instructions from the README file.
I downloaded the .fa files, I created the executable files by using the makefile
and I used the command python
I don't really understand the part:
"use in the usual way to access the data"
So... what is the "usual way"? what do I do from this point to get my mappability_map.txt file?

Thanks in advance to anyone that will try to help.
AL_B is offline   Reply With Quote
Old 01-29-2014, 04:28 AM   #2
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Location: poland

Join Date: Jan 2014
Posts: 4

It took me a while to find answer for that one myself, before I decided to simply look at the code. I figured out you should run script, but first - you need to edit it, because the original version is suitable for human chromosomes. For example, my data consist from seven chromosomes named 1, 2, 3, 4, 5 and Mt, Pt. So I changed the beginning of the code to look like that:

for i in xrange(1,8):
  if i<= 5:
    chr = str(i)
  elif i ==6:
    chr = "Mt"
    chr = "Pt"
Also, I removed "chr" from next lines:
nicechr = chr
filename = chr + "b.out"
beacuse my files' names don't start with "chr".

Then I simply run
python > map.txt
in the same directory where the script were and all files generated by

I'm not positive if this is correct way to do that, because in the next step I get some weird errors, but I think it's not because of the mappability file.
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