Mappability tracks for danRer7 and galGal4

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Adira Mollari

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Aug 21, 2014, 11:35:56 AM8/21/14
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Hi,
I'm trying to generate the mappability files for the zebrafish (danRer7) and chicken (galGal4) genomes. I have downloaded the genome from UCSC genome browser and split it into individual files for each chromosome/scaffold using a python script, such that each file contains a fasta header and the sequence and the name of the header is in the filename. I then ran make which generated the three executables: chr2hash, oligoFindPLFFile and mergeOligoCounts and then added their location to my path. However, when I run compile.py . I get 'Segmentation fault' error messages with the last script:
oligoFindPLFFile chr1.fa chr1.fa . 0 0 1 1 > chr1xchr1.out 
/bin/sh: line 1: 14190 Segmentation fault oligoFindPLFFile chr1.fa chr1.fa . 0 0 1 1 > chr1xchr1.out
Could you please let me know whether I'm doing something wrong? 
Thanks, 
Adira

Dongjun Chung

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Aug 28, 2014, 4:40:46 PM8/28/14
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Hi Adira,

Overall, what you did looks OK to me.

In this case, you might need to directly contact Gerstein Lab, who developed MappabilityMap.
The contact information can be found in http://info.gersteinlab.org/PeakSeq.

Hope that it helps.

Best,
Dongjun



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