https://github.com/txje/sequence-bias-adjustment

Method and utilities for reweighting sequence read counts to adjust for nucleotide bias from assay or sequencing
https://github.com/txje/sequence-bias-adjustment

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Method and utilities for reweighting sequence read counts to adjust for nucleotide bias from assay or sequencing

• Host: GitHub
• URL: https://github.com/txje/sequence-bias-adjustment
• Owner: txje
• License: mit
• Created: 2014-06-10T18:18:17.000Z (about 10 years ago)
• Default Branch: main
• Last Pushed: 2020-06-18T16:03:50.000Z (about 4 years ago)
• Last Synced: 2024-02-12T23:48:31.276Z (5 months ago)
• Language: Python
• Size: 438 KB
• Stars: 4
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

Lists

• awesome-atac-analysis - sequence bias correction

README

        
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       [--resume ]

      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)