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Any database with RNA-Seq signal files for GTEx data?

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
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written by thejustpark thejustpark

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!

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written by thejustpark thejustpark

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

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written by ATpoint ATpoint

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

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written by thejustpark thejustpark

1 answer

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)

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written by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup

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!

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written by thejustpark thejustpark

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