Pipelines or softwares used for data analysis in this papaer.
**Content: **
MethylC-seq: simple nextflow for methylation analysis wrote from scratch.
pipeline for MethylC-seq analysis was wrote from scrate by simply assembling suite of softwares into nextflow mode. Analysis workflow was described in methods section of Papareddy et al 2020 Genome biology.
Assuming configures files were optimized for your computing cluster, run command:
nextflow run main.nf --files '/PATH/TO/FASTQ' --annot '/PATH/TO/TAIR10.fa' --output '/PATH/TO/OUTDIR'
should do the job.
ChIP and RNAseq analysis was based on nf-core curated pipeline. However modifications were made to implement pipeline on VBC-HPC
ChIP-Seq: Modified from nf-core/chipseq v1.2.1 - Platinum Mole.
RNA-seq: Used as is from nf-core/rnaseq v2.0 - Titanium Tiger.
Rscripts for ploting asthetics.