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

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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

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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

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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: [email protected]