Question: Downloading public RNA-seq raw read counts
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7 months ago by
A3.5k
A3.5k wrote:

Hi,

I am seeking RNA-seq raw read counts for Oesophageal adenocarcinoma

Here I am not seeing any OESO

https://www.synapse.org/#!Synapse:syn2812961

In this link I selected some OESO but I don't know how to download

https://portal.gdc.cancer.gov/exploration?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22Adenomas%20and%20Adenocarcinomas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22Esophagus%22%5D%7D%7D%5D%7D

And finally here https://confluence.broadinstitute.org/display/GDAC/Download

I need public RNA-seq raw read counts for this cancer especially some normal samples as I need normal sample to remove stromal contamination

Any help please?

nih rna-seq tcga firehose • 261 views
ADD COMMENTlink written 7 months ago by A3.5k
1

How about: https://www.cbioportal.org/datasets. Here is a direct link but verify before you download.

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax73k

Thank you so much looks the same I need but normalized one so for PCA and DE by DESeq2 I must convert normalized counts to raw counts

ADD REPLYlink written 7 months ago by A3.5k

https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/302

ADD REPLYlink written 7 months ago by A3.5k
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