GETx patient RNA_Seq read count download
I'm trying to download the STAD tissue RNA-Seq read count of individual patients. I didn't find any link / source to directly download the tissue specific data
Example
P_ID P1 P2 P3 Pn..
Gene1/trns 12.0 5.0 0 ....n
Gene2 /trans 7.0 50.0 15.0 ....
Gene3/trans 0.00 10.0 12.0 ....
I want to download the STAD normal tissue in this format.
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Kristoffer Vitting-Seerup
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skjobs
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skjobs
1 answer
From the official GTEx website you can download a lot of data. From your description it sounds like you need the "Gene read counts" file which you can find here. Paired with the sample and subject annotation file you can easily subset to the tissue of interest.
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Do you want to download the TCGA data or something else...?
It's not the TCGA data, It's something else. It's GTEx data has only normal tissue expression. In TCGA there are very few number of normal samples. In GTEx has larger number of normal as compare to TCGA.