mappability-track-pipeline

Generate mappability tracks as BigWig file from genome fasta with GEM

Requirements

• gem-indexer, gem-mappability and gem-2-wig from the GEM library.
• Python2 (>=2.6)
• bedGraphToBigWig from UCSC Kent utilities.

Settings

Edit config.sh to specify paths to the required binaries and a number of max mismatches to calculate mappability (default=2, following UCSC mappability tracks).

wig-filter

wig-filter.py filters Wig variableStep tracks which have scores lower than specified score and output a Wig or bedGraph format file.
By default, this script passes only score=1 (uniquely mappable) regions.

Work with Sun/Univa Grid Engine

01-make-gem-index.sh, 02-make-mappability.sh

If a number of threads is not specified, these scripts use NSLOTS variable as the number of threads.

02-make-mappability.sh, 03-get-bigwig.sh

If a read length is not specified, these scripts use SGE_TASK_ID variable as the read length.