A pipeline integrated data analysis and valuation for wheat ATAC-seq

###install dependencies

conda create -n wheatATAC

conda activate wheatATAC

conda install -c bioconda macs2

conda install -c bioconda bowtie2

conda install -c bioconda fastqc

conda install -c bioconda samtools

conda install -c bioconda idr

conda install -c bioconda phantompeakqualtools

conda install -c bioconda trimmomatic

conda install -c bioconda deeptools

conda install -c bioconda bedtools

conda install -c bioconda ucsc-bedtobigbed

conda install r=3.6 ##The verson of R must >=3.6

###2.analysis the ATAC-seq dataset

Usage: sh analysis.sh work_dir trimmomatic_adapter_dir wheat_reference_dir

notice: The fastq file are in *_R1_fq.gz

##2.1 make meta files

The format of meta files are like following. The first column lists the sample name, the second column are the repeats information of samples, and the last column lists the corresponding prefix of the fastq files. The file we named ATAC.txt here.

#with repeats and without inputs:

sampleA sampleA_rep1 C1

sampleB sampleA_rep1 C2

sampleC sampleA_rep1 C3

...

#with repeats and without inputs:

sampleA sampleA_rep1 C1

sampleA sampleA_rep2 C2

sampleB sampleB_rep1 C3

sampleB sampleB_rep2 C4

...

#with repeats and with inputs:

sampleA sampleA_rep1 C1

sampleA sampleA_rep1_control N1

sampleA sampleB_rep2 C2

sampleA sampleB_rep2_control N1

##2.2 trim, alignment, remove unmapped and duplicate reads

#note that the adapter file is user definded, please use vi align.sh to replace it.

##2.3 prepare file for IDR analysis

##2.4 peak calling, idr analysis and consistent peaks acquirment

###data valuation

sh valuation.sh

#The process of data valuation contains file convert for IGV visualization, FRiP and SPOT calculation, TSS enrichment analysis, peak annotation, samples correlation analysis and signal comparasion.

README.txt