Where can I find bisulfite sample data to practice trimming, mapping and methylation call? Im new in this field

Question

[Pin.Bioinf]

Hello, I am learning to analyze bisulfite reads analysis: trimming mapping and methylation calls Is there any data available for learning? Also, are trim galore and bismark the most used softwares or are there better alternatives? Any good websites I should look at for theory aswell?

Thank you very much

Answer 1

[Joseph Hughes]

From the paper Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications, the data is available here: https://www.ncbi.nlm.nih.gov/geo/roadmap/epigenomics/

Also the following study which compare nanopore methylation detection to bisulfite sequencing: Detecting DNA cytosine methylation using nanopore sequencing, there are links to their own samples used for benchmarking which can be found here: https://www.ebi.ac.uk/ena/data/view/PRJEB13021