Question: Any database with RNA-Seq signal files for GTEx data?
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gravatar for thejustpark
14 months ago by
thejustpark80
United States
thejustpark80 wrote:

I am trying to analyze RNA-Seq data in GTEx. I learned that, although BAM files are restricted and require access control, its signal files are not identifiable, thus possibly in the open domain. Do you know of any database or download sites from which I can download RNA-Seq signal files (either in bigwig or bedgraph) for each sample in each tissue?

I know that UCSC GTEx Signal Hub (http://hgdownload.soe.ucsc.edu/hubs/gtex/gtexHub.html) kinda has that. But I figured that there is one bigwig for each tissue, probably merging all individual RNA-Seq signals for the tissue.

Thank you very much in advance,

rna-seq • 447 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by thejustpark80

Thank you kristoffer.

I am now checking recount2 to download bigwig files for each sample. Since I need individual bigwig files, I don't need to worry about summing to tissue-level signals. Thank you again!

ADD REPLYlink written 14 months ago by thejustpark80

Please use ADD REPLY for comments to keep the thread organized. Thank you.

ADD REPLYlink written 14 months ago by ATpoint40k
1

Thank you ATpoint for your help! Now I see how to use this thing.

ADD REPLYlink written 14 months ago by thejustpark80
1
gravatar for kristoffer.vittingseerup
14 months ago by
European Union
kristoffer.vittingseerup3.4k wrote:

I think the closes you can get is though recount2. Try playing around with the associated R package vignette - they provide some coverage measures. But you will probably have to sum to tissue-levels yourself (remember to normalize)

ADD COMMENTlink written 14 months ago by kristoffer.vittingseerup3.4k

Thank you kristoffer.

I am now checking recount2 to download bigwig files for each sample. Since I need individual bigwig files, I don't need to worry about summing to tissue-level signals. Thank you again!

ADD REPLYlink written 14 months ago by thejustpark80
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