Closed abearab closed 11 months ago
I am not exactly sure about how to get the data into IGV as we have used Seqmonk for this purpose in the past, see e.g. here: https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=4965689_f1000research-5-9980-g0002.jpg
Here are some more examples on how to get started with methylation analysis in SeqMonk: https://www.bioinformatics.babraham.ac.uk/training.html#bsseq. It is really dead-easy as SeqMonk simply accepts Bismark coverage files (.cov.gz
) as input, so you can literally get a figure as the one shown above in the matter of a few minutes.
Thanks for your response! One dumb question, the expected .cov.gz
file is the output of bismark_methylation_extractor
command, right? How would you use it (i.e. what options)?
It is indeed, just use the option --bedGraph
for the methylation extraction. Or --help
for more info. Here are the docs: https://felixkrueger.github.io/Bismark/bismark/methylation_extraction/
Okay, that's the bedGraph
file. Thanks
The coverage file is pretty much the same as the bedGraph file, but in addition contains the counts methylated and unmethylated cytosines.
Hi @FelixKrueger – I have another question! I could solve my issue here https://github.com/FelixKrueger/Bismark/issues/633 and now I'm trying to show a close-ups of genomic region of interest, something like this plot:
Fig 2F. https://doi.org/10.1016/j.cell.2021.03.025 (@hovestadt's original work)
I don't know the right way to prepare the CpG methylation info from
bismark
outputs for building this visualization. Do you have any recommendation? Thanks agin for sharing your expert advice.