Downloding only RNA-Seq Raw counts data from ICGC

Question

[David_emir]

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

[lakhujanivijay]

I tried using dplyr but I am not able to get in the proper format.

Share you code here

[David_emir]

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

[ATpoint]

Share you code here

[David_emir]

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

Thanks for your help

Answer 1

[David_emir]

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