Question: What is common source of DNA- methylation raw data read files?
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gravatar for ak259369
7 months ago by
ak2593690
ak2593690 wrote:

I am new bie in DNA methylated world and looking for general source for raw data read files for applying to some methylation analysis tools. Please help me by sharing the link for that.

Thanks

dna-methylation • 281 views
ADD COMMENTlink modified 7 months ago by Charles Warden6.6k • written 7 months ago by ak2593690
1
gravatar for genomax
7 months ago by
genomax66k
United States
genomax66k wrote:

Sequence data (including DNA-methylation) can be found in two public repositories. NCBI SRA and EBI-ENA.

ADD COMMENTlink modified 7 months ago • written 7 months ago by genomax66k
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gravatar for Charles Warden
7 months ago by
Charles Warden6.6k
Duarte, CA
Charles Warden6.6k wrote:

You can also deposit SRA data (the raw .fastq.gz files) through GEO, to have linked processed data sets.

I'm not sure if you are looking for a specific type of BS-Seq data, but there is also microarray DNA Methylation data in GEO (Illumina Array, MeDIP, etc.).

For arrays, you can search for specific platforms within GEO: https://www.ncbi.nlm.nih.gov/geo/browse/

Otherwise, the platform is probably the sequencing technology; so, you would want to search for "BS-Seq," "RRBS," etc among the data sets: https://www.ncbi.nlm.nih.gov/geo/

ADD COMMENTlink written 7 months ago by Charles Warden6.6k
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