Bismark-guide.md

Canonical Guide to using Bismark

See also the official documentation.

User Guides

1. http://felixkrueger.github.io/Bismark/Docs/
2. https://www.bioinformatics.babraham.ac.uk/projects/bismark/

Use cases from our lab

https://github.com/RobertsLab/code/blob/master/20-bismark.sh

• https://github.com/sr320/paper-oly-mbdbs-gen/blob/master/code/00-Bismark.sh - used to processes BS-MBDSeq Data from Olympia oysters, run on Mox. Author: Steven Roberts

• https://raw.githubusercontent.com/laurahspencer/C.magister_methyl-oa/master/scripts/20201214_Cmag_bismark-align.sh - slurm script used to process MiSeq data from Dungeness crab, run on Mox. Here is a Jupyter Notebook with more details/narrative. Author: Laura Spencer, but derived from the MethCompare workflow.

• https://github.com/sr320/paper-oly-wgbs/blob/master/submission/Narrative.Rmd part of Rmd narrative, used for WGBS Olympia oyster data. Author: Steven Roberts

• https://github.com/hputnam/Geoduck_Meth/blob/master/code/03-bismark.sh geoduck environmental memory project. Run on Mox. Author: Steven Roberts

• https://raw.githubusercontent.com/epigeneticstoocean/paper-gonad-meth/master/code/02-bismark.sh eastern oyster data, run on Mox

Diagram