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How to extract CpG level for IGV plot #636
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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 ( |
Thanks for your response! One dumb question, the expected |
It is indeed, just use the option |
Okay, that's the |
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 #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.The text was updated successfully, but these errors were encountered: