Analysis of whole-genome bisulfite sequencing (WGBS) data.

This pipeline is being developed for the analysis of a particular data set, with the hope that it may be useful for the analysis of other data sets.

The pipeline currently includes {scripts}:

• ✅ Checksum of downloaded files (sum) {001}
• ✅ Control quality of raw FASTQ files (FastQC) {002}
• ✅ Merge raw (paired-end) FASTQ files from multiple sequencing runs for each biological replicate (cat) {003}
• ✅ Control quality of merged FASTQ files (FastQC) {004}
• ✅ Trim adapter and low-quality bases from merged FASTQ files (Trim Galore!) {005}
• ✅ Control quality of trimmed FASTQ files (FastQC) {006}
• ✅ Report of trimming statistics {007}
• ✅ Alignment of trimmed read pairs to bisulfite-converted genome (Bismark) {008}
• ✅ Control quality of aligned BAM files (FastQC) {009}
• ✅ Report of alignment statistics {010}
• ✅ Deduplication of aligned read pairs (Bismark) {011}
• ✅ Control quality of deduplicated BAM files (FastQC) {012}
• ✅ Report of deduplication statistics {013}
• ✅ Extraction of methylation calls from deduplicated aligned read pairs (Bismark) {014}
• Upcoming 🔴 Report of methylation extraction statistics {015}
• ✅ Addition of read group, sorting and indexing of BAM files (Picard) {016}
• ✅ Combined Bismark report in HTML format (Bismark) {017}
• ✅ Import methylation calls and format GRanges for subsequent analyses (bsseq/Bioconductor) {018}
• ✅ Import coordinates of unmasked CpG islands (CGI) and format as GRanges (UCSC tracks) {019}
• ✅ Import coordinates of genes and format as GRanges (biomaRt/Bioconductor) {020}
• ✅ Overview of CGI coverage in the imported data set {021}
• ✅ Identification of differentially methylated regions (DMRs) (bsseq/Bioconductor) {021}

• Bismark: using v0.15.0 cloned from GitHub to benefit of a recent bug fix allowing the proper use of the --cytosine_report option of the script bismark_methylation_extractor. The bug fix is not yet available in the version available on the Bismark website