How To Convert A Genome Mappability Data (Gem-Mappability) To Ucsc Compatible Format?

Question

[Bojan]

I am trying to calculate genome mappability of some yeast species using GEM-mappability (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377) which was used for the calculation of the USCS Genome Browser mappability tracks. However, I cannot figure out how to convert output file (output format: http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=Gem_mappability_man_page ) into format compatible with USCS Genome Browser (BED, bigBed, bedGraph, GFF, GTF, WIG, bigWig, MAF, BAM, BED detail, Personal Genome SNP, VCF, or PSL formats). Any suggestions? Thanks in advance.

Example of the output:

  ~~ENCODING
   ' '~[0-0]
   '!'~[1-1]
   '"'~[2-2]
   ...
   '&'~[6-7]
   ...

and

  ~chr17
   !!!!!!!!!!!!!!!!!!!!!!!!!""!!!!!!!!!!%%*&&00,00/66/140.-,,
   ,/04:41237?CDDDD??>;7*$$"""""""!!!!!!!!!!!!!!!!!!!!!!!!!!!
   !!!!!%$$#!!"#$&%"#.7>:><9898899999:.3---1111"!!!!##"""""!!
   ...

[Istvan Albert]

I have sent the author a message via the Messaging link.

[Malachi Griffith]

Seems like that link to the man page does not work... Can you post an example of the output you are getting?

[Bojan]

I have replaced the old link to the man page with the correct one.

Answer 1

[bioinformatica]

Hi there, Just in case someone is looking for the same answer. The link mentioned in one of the answers is empty http://algorithms.cnag.cat/wiki/FAQ:Generating_mappability_tracks

You can create the BigWig file as follows: 1) Get the mappability file with gem-mappability 2) Use gem-2-wig to obtain a wig file 3) Convert the wig file into a BigWig file with the wigToBigWig tool from the UCSC. This tool can be downloaded from their website http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

I could not find any other way to walk around this problem.

Sheila

[pyjiang2]

I found many of the above links don't work. Maybe there's a change in their website. I found this useful post which includes steps to generate wig file, which steps follow Sheila's description.

https://wiki.bits.vib.be/index.php/Create_a_mappability_track

Answer 2

[brentp]

The FAQ page tells you how to create a wig/bigWig, which is viewable in the browser:

http://algorithms.cnag.cat/wiki/FAQ:Generating_mappability_tracks