Downloading public RNA-seq raw read counts
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2.1 years ago
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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?

RNA-Seq TCGA firehose NIH • 529 views
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How about: https://www.cbioportal.org/datasets. Here is a direct link but verify before you download.

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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

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