Question: How To Convert A Genome Mappability Data (Gem-Mappability) To Ucsc Compatible Format?
1
gravatar for Bojan
5.2 years ago by
Bojan10
Bojan10 wrote:

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"!!!!##"""""!!
   ...
• 3.9k views
ADD COMMENTlink modified 8 months ago by bioinformatica10 • written 5.2 years ago by Bojan10
1

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

ADD REPLYlink written 5.2 years ago by Istvan Albert ♦♦ 75k

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

ADD REPLYlink written 5.2 years ago by Malachi Griffith16k

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

ADD REPLYlink written 5.2 years ago by Bojan10
1
gravatar for bioinformatica
8 months ago by
bioinformatica10 wrote:

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

ADD COMMENTlink written 8 months ago by bioinformatica10
0
gravatar for brentp
4.4 years ago by
brentp22k
Salt Lake City, UT
brentp22k wrote:

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

ADD COMMENTlink written 4.4 years ago by brentp22k
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