calculate mappability of a genome

I couldn’t find a simple explanation of how to run gem_mappability as was carried out in Catoni et al. 2017 EMBO (out of the Paszkowski lab). I found enough information here to get me going – below is the simplified version for those that simply want to get a bigwig or bedgraph of these values but don’t care about comparing a bajillion different k-mer sizes.

  1. download the compressed file (your specific version may be different)
  2. tar -xvjf GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2
  3. cd GEM-binaries-Linux-x86_64-core_i3-20130406-045632/
  4. cp all the executables in ./bin to a directory in your path, such as /usr/local/bin
  5. then run the following – change the names of your files accordingly:

gem-indexer -i /path_to_your_genome_fasta -o output_name_you_pick

gem-mappability -I output_from_above -l [you decide how big kmer should be] -o pick_a_gem_output_name

gem-2-wig -I gem_indexer_output -i gem_mappability_output -o your_wig

then convert your wig to bigWig using Jim Kent/UCSC tools

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