Man pages for anilchalisey/chompR
ChIP and ATAC-seq data processing pipeline

align_dnaAlignment of DNA-seq reads
annotate_peaksAnnotation of peaks
build_indexBuild insex for HISAT2
cc_chipCreate cross-correlation plots for ChIP-seq data
chainLiftOver chain file in rda format for conversion from hg38 to...
check_sampleCheck that targets file contains the necessary info in the...
consensus_peaksConsensus peaks
create_bwCreate bigwig files
deseq2_analysisRun DESeq2 analysis on ChIP/ATAC-seq count data
exploratory_analysisExploratory analysis of DESeq2 data
fl_atacCreate fragment size plots for ATAC-seq data
make_MACreate MA plot
make_PCACreate PCA plot for transformed data
make_screeCreate scree plot from prcomp data
peak2GrangesFile conversions
pipePipe operator
plot_peaksummaryPlots of peak width and distance to TSS
qc_alignmentGenerate some alignment statistics on reads
qc_alignment2Perform alignment statistics on reads
run_atacRun ATAC-seq analysis
run_chipRun ChIP-seq analysis
run_fastqcQC reports for fastq files using FastQC
run_featurecountsCount reads in bam files using featureCounts
run_greatGREAT analysis
run_hisat2Wrapper script to run HISAT2.
run_macs2Perform peakcalling with MACS2
run_multiqcGenerate MultiQC report for FastQC
run_sambambadupMark duplicates in BAM file
run_samsortWrapper scripts for SAMtools functions
sanity_checkImport the metadata and check it is correct
shift_bamShift ATAC-seq reads
trim_fastqAn R-based wrapper for fastp
anilchalisey/chompR documentation built on Sept. 28, 2018, 8:01 a.m.