/ATACseqMappingPipeline

Primary LanguageShellGNU General Public License v3.0GPL-3.0

ATACseqMappingPipeline

RRID: SCR_017558

  • This Pipeline is designed to map ATAC-seq data to large genome, for example, for wheat.

  • It splits large genome files into parts and do the mapping and then finally merge them

Descriptions

1. Fastqc, trimglore, trimmomatic to clean reads

2. Merge Genome+CtDNA+mtDNA, Split Genome fasta, and bowtie index

3. Bowtie mapping, merge, re-coordinate, sort and rmdup the BAMs

4. BAM to BAMPE, then to BEDPE, MACS2 callpeaks

Requirements

  • Linux: grep, perl, cut, sort, echo, cat, echo

  • trimmomatic

    export TRIMMOMATIC_ROOT=${PROGPATH}/trimmomatic/v0.39/x86_64

    export TRIMMOMATIC_ADAPTORS=${PROGPATH}/trimmomatic/v0.39/x86_64/adaptors

    export TRIMMOMATIC_JAR=${PROGPATH}/trimmomatic/v0.39/x86_64/trimmomatic-0.39.jar

    export CLASSPATH=${PROGPATH}/trimmomatic/v0.39/x86_64/trimmomatic-0.39.jar:$CLASSPATH

  • trim_galore

  • picard_tools

  • Bowtie

  • BEDtools

  • SAMtools

  • bamaddrg

  • FuhaoBin:

    FuhaoBashModulesbam_filter_by_readname_file.pl

    bam_restore_splited_coords.pl

    fasta_splitter.pl

    macs2_bedpe_from_bampe.sh

Options

See '-h' for help

  1. Trim and clean reads

  2. atac.2.index.split.sh

  3. atac.3.bowtie.mapping.sh

  4. atac.4.macs2peaks.sh

Examples

Author:

Fu-Hao Lu

Post-Doctoral Scientist in Micheal Bevan laboratory

Cell and Developmental Department, John Innes Centre

Norwich NR4 7UH, United Kingdom

E-mail: Fu-Hao.Lu@jic.ac.uk