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Downloding only RNA-Seq Raw counts data from ICGC

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
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written by David_emir David_emir

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

Share you code here

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written by lakhujanivijay lakhujanivijay

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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written by David_emir David_emir

Share you code here

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written by ATpoint ATpoint

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

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updated by ATpoint ATpoint • written by David_emir David_emir

1 answer

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

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written by David_emir David_emir

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