Tutorial for analyzing WGBS data

Question

[pt.taklifi]

Is There a comprehensive tutorial for aligning and methylation calling of BS converted data? I understand that methylseq is a widely used pipeline but I did not find a good tutorial for that.

Thank you in advance

[GenoMax]

Here is a downstream tutorial: https://nbis-workshop-epigenomics.readthedocs.io/en/latest/content/tutorials/methylationSeq/Seq_Tutorial.html

[pt.taklifi]

Thank you for your response. I'm looking for a tutorial with more focus on upstream steps, like alignment to genome and 5mC calling, etc

Answer 1

[Papyrus]

Regarding general concepts I'm very fond of the Canadian Bioinformatics Workshop videos (such as this one), and if you combine that with the documentation for the Bismark pipeline, which basically covers and explains all the upstream steps and critical points, I think that you can get a good grasp on the upstream analyses even if later on you use other tools.

[pt.taklifi]

Thank you for the references

[pt.taklifi]

On the same note, do you have any suggestions on removing adapters from WGBS reads; since unmethylated Cs in adapter sequence are converted to Ts, Im not sure the fastQC adapter contamination report is very reliable.