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I'm trying to analyise methylation data using GEO, in order to conduct a multi-omics analysis. The SubSeries I am referring to is GSE73303. Unfortunately, the code used to inspect it produces empty file, so I downloaded tar files, as I found on bioconductor forum (ref. this).

I was able to download the tar files and extract thenm but afterwards I got a list of .bigwig files. I tried to read them on R, but actually I feel very lost and I can't understand how to trace back methylation data from these files.

If someone can guide me into this process, it would be really appreciated

Thanks in advance

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  • $\begingroup$ If I've not already said this welcome to the site. The answer below is reasonable because generally we rarely provide overviews or manuals in the answer. What you need to do is break the question down to individual parts that don't work - divide and conquer - and provide the code for each stage. At present this isn't a cool question for this site because it's too broad. I hope that helps. In other words submit multiple focused questions rather than a very general question requesting an unspecified amount of help. $\endgroup$
    – M__ ♦
    Commented Jul 22, 2023 at 14:11
  • $\begingroup$ Ok I modify it based on your suggestion, thanks $\endgroup$
    – Riesz98
    Commented Jul 22, 2023 at 14:30

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As I've already told you here GEO Methylation dataset "GSE73303" shows 0 features GEO/GEOquery does not provide ready-to-use processed NGS data. It can be that the authors provide processed data, but if not (apparently not the case in this submission) then you have to start from the fastq files. Please see the many tutorials online on downloading fastq and processing bisulfite data, or try to use existing pipelines (nf-core methylseq might be an option) or seek a collaboration.

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  • $\begingroup$ Yes I saw your reply thanks. I was just wondering, since I'm not an expert, if it was possilbe to follow the approach suggested in the reference that I linked. $\endgroup$
    – Riesz98
    Commented Jul 22, 2023 at 13:59
  • $\begingroup$ @Riesz98 it would be etiquette to upvote. $\endgroup$
    – M__ ♦
    Commented Jul 22, 2023 at 14:07

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