CSE_pipeline

Process to generate Chromatin State Expression (CSE) matrix

This pipeline takes in bam files from bulk RNA-seq data generated by the nf-core and generates a Chromatin State Expression matrix. The annotations are based on the full stack ChromHMM annotations from here.

Required tools

1. snakemake
2. bedtools
3. R
4. MACS3
5. Subread package, specifically featureCounts

Instructions

1. Copy or link bam files to a folder called data.
2. List the sample names (no .bam suffix) as individual lines in the text file sampleNames.txt.
3. Run snakemake command

Output

1. DNX_data_count_anno.tsv contains the counts for each chromatin state feature (rows) for each sample (columns).
2. peakCountBySample_broadPeaks folder contains the MACS3 peak calling outputs for each samples for both + and - strands.
3. peakCountBySample_broadPeaks_gtf folder contains peak annotations in gtf format.
4. peakCountBySample_broadPeaks_featureCounts contains counts for each peak feature, annotated with chromatin states, for each sample.