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leekgroup / recount-website

Code for the Recount project
https://jhubiostatistics.shinyapps.io/recount/
MIT License
11 stars 5 forks source link

Availability of bigwig files? #26

Closed cmdcolin closed 2 years ago

cmdcolin commented 3 years ago

Hi there,

Do you have the bigwig files for recount available? I tried to manually stitch together what I thought the link format might be e.g.

http://duffel.rail.bio/recount/v2/SRP042161/mean_SRP042161.bw

this is a 404 however

Separate issue here from the google chrome just to stay on target :)

cmdcolin commented 3 years ago

Just in case it helps gauge how I approach the recount project, I'm just looking for interesting examples of single cell data to plot, and thought recount might be a good example of precomputed data for this!

lcolladotor commented 2 years ago

Hi,

Thank you for your interest in the recount2 project (recount R package).

You can use download_study() to get download the per-sample BigWig files https://github.com/leekgroup/recount/blob/master/R/download_study.R#L34. You could also use the newer recount3 project and find the URLs using create_rse()$BigWigURL like at http://research.libd.org/recount3/reference/create_rse.html.

Best, Leo