Question: how to search and get bisulfite-sequencing fastq files
gravatar for parra.sev
6 weeks ago by
parra.sev0 wrote:

I'm getting started in bioinformatics and I want to study some methylation profiles in different organism, but first I need to obtain bs-seq fastq files for mapping reads against a reference genome using Bismark; I got a test dataset from the Bismark website, but I want to know how to search and obtain that type of fastq files, in single and paired-end format, and I'm not sure what database to use (I'm trying with GEO, but I'm not familiar with how that database works; besides, I'm not sure which parameters to use in query (should I search 'methylation profiling by array'? by 'high throughput sequencing'?), so I'd really appreciate any help for someone just starting to work with this kind of data.

ADD COMMENTlink written 6 weeks ago by parra.sev0
gravatar for genomax
6 weeks ago by
United States
genomax85k wrote:

Use sra-explorer to search for datasets. See: C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by genomax85k

thank you so much, I'm using it and it works perfectly!

ADD REPLYlink written 6 weeks ago by parra.sev0
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