Correcting nucleotide-specific bias in high-throughput sequencing data

Reweight high-throughput sequencing reads to account for nucleotide-specific bias from any source, including assay and sequencing biases.

Requirements:

• samtools (in PATH)
• Python (2.7)
  • numpy
  • pysam
  • matplotlib (pyplot)

Installation:

git clone http://github.com/txje/sequence-bias-adjustment
cd sequence-bias-adjustment

Usage:

sh seqbias_pipe.sh <ref> <chroms> <bam> <k> <outdir> <prefix> [--resume <step>]
  ref           reference genome FASTA file
  chroms        list of chromosomes (one per line) to correct
  bam           should be aligned and filtered to mask repetitive elements and such (if needed)
  k             tile size to correct (5 is recommended most of the time)
  outdir        directory to put all output files
  prefix        prepended to all intermediate and output files

Example -- to run bias correction on an example ENCODE DNase-seq data set:

git clone http://github.com/txje/sequence-bias-adjustment
cd sequence-bias-adjustment
mkdir example_data
cd example_data
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12878AlnRep1.bam
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12878AlnRep1.bam.bai
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa
chmod 700 twoBitToFa
./twoBitToFa hg19.2bit hg19.fa
cd ..
sh seqbias_pipe.sh example_data/hg19.fa example_data/hg19.chrom.sizes example_data/wgEncodeOpenChromDnaseGm12878AlnRep1.bam 5 example_results gm12878.dnase

Jeremy Wang, Ph.D.
Department of Genetics
University of North Carolina at Chapel Hill

MIT License (see LICENSE.txt)