Downloding only RNA-Seq Raw counts data from ICGC
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2.8 years ago
David_emir ▴ 390

Hi,

I wanted to download RNA-Seq raw counts data from ICGC with samples as columns and gene_symbol as row names. I tried using dplyr but I am not able to get in the proper format. It would be of great help to me if you guys can let me know how to download this.

Sincerely,

Dave

P.S: any package in R would be helpful

ICGC RAW counts • 1.0k views
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I tried using dplyr but I am not able to get in the proper format.

Share you code here

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Thanks Vijay, I tried to cut and paste sample_id rows as a column but it gave me a really messed up results.

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Share you code here

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Hope this will help others, code is here.

mlr --tsv cut -o -f id4,id1,count2 then reshape -s id1,count2 input.tsv


Or

datamash --header-in --whitespace crosstab id4,id1 unique count2 < file


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Entering edit mode
2.8 years ago
David_emir ▴ 390

Thanks a lot, Guys, I got a solution for this for cross-tabulation (or pivot table) using GNU Datamash and with Miller, using reshape!

Dave