Alignment and methylation calling for reduced representation or whole genome bisulfite sequencing data.
- For WGBS, trim adapters and low quality bases (Trimmomatic).
- For RRBS, trim adapters, low quality bases, and the cytosine artificially introduced in the end-repair step during the library preparation (Trim Galore).
- Align to the bisulfite converted reference genome (Bismark and Bowtie2).
- For WGBS, remove duplicate reads (Bismark).
- Extract methylation calls (Bismark).
- Generate graphical report for alignment, deduplication, and methylation extraction (Bismark).
- Generate methylation calls genome browser tracks.
Set up a new analysis (common across all routes).
cd <project dir> git clone --depth 1 https://github.com/igordot/sns sns/generate-settings <genome> sns/gather-fastqs <fastq dir>
Check for potential problems.
grep "ERROR:" logs-sbatch/*
BAM-Bismark: Alignment files.
BIGWIG-Bismark: Methylation ratio bigWig files. Can be used for visual inspection as genome browser tracks.
meth-Bismark-*: Methylation calls.
summary-combined.rrbs.csv: Summary table that includes the number of reads, alignment rate, fraction of PCR duplicates, number of covered Cs, and Cs methylated in different contexts.
Bismark-report: Graphical report for Bismark steps (alignment, deduplication, and methylation extraction).