Bismark Report Merging

Question

[maxrhighsmith]

I am running Bismark to perform methylation analysis on whole-genome bisulfite sequencing data. To speed up the process I am splitting the paired fastq files into multiple smaller files and aligning them in parallel. I am able to successfully remerge the bam files, dedup, and run the bismark_methylation_extractor tool. I want to use the bismark2report tool, however, it requires a single alignment_report as input. Because of the parallel processing, I have separate alignment reports for each group of split pairs. Is there an existing script that merges these alignment reports into one file that can be read by bismark2report --alignment_report <file>?

[fu_entomology]

Hi maxrhighsmith , did you get this sorted out?