Question: Downloading public RNA-seq raw read counts
0
gravatar for A
16 months ago by
A3.8k
A3.8k 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 • 383 views
ADD COMMENTlink written 16 months ago by A3.8k
1

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

ADD REPLYlink modified 16 months ago • written 16 months ago by genomax87k

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 16 months ago by A3.8k

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

ADD REPLYlink written 16 months ago by A3.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1819 users visited in the last hour