How can I add Whole Exome Sequencing (WES) from a sample in TCGA?

Posted in TCGA data on the CGC by HoJoon Lee Thu Jan 28 2016 23:11:52 GMT+0000 (UTC)·2·Viewed 984 times

Hi, If I want to run a program on a WES from TCGA-CG-5720 in TCGA STAD, how can I add this one bam file to a Project? Nothing came ot when I typed "TCGA-CG-5720" in search window. Do you have any idea? Thanks, HoJoon
Gaurav Kaushik
Jan 29, 2016

Hi HoJoon,

You can use the Data Browser (located under the 'Data' tab) to interactively find the BAM files for this patient. Here is a link to a screenshot of the query: http://i.imgur.com/W8CI8SD.png
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In this query, you're searching for Files that have the Experimental Strategy as 'WXS' and Samples that have the Sample ID 'TCGA-CG-5720'. You can learn more about building queries with the Data Browser at http://docs.cancergenomicscloud.org/docs/the-data-browser.

Once the query is built, you'll see the BAM/BAI files in the table below, as in this image: http://i.imgur.com/f6WY88t.png

You can then click '+ Copy Files to Project' to add these to any Controlled Data Project that you have created.

Please feel free to reach out to us with any further questions.

Brandi Davis-Dusenbery
Jan 29, 2016

Hi HoJoon!
Thanks so much for your question - a couple more thoughts:

Currently the search box allows you to enter any UUID as these are considered the primary ID on all entities. (you can read more about UUIDs vs barcodes at https://wiki.nci.nih.gov/display/TCGA/Universally+Unique+Identifier#transition)

You can also enter a comma separated list of UUIDs into the search box which allows you to find multiple entities at once.

One additional note, the barcode you provide is actually a CASE barcode, which has the sample barcodes: TCGA-CG-5720-01A and TCGA-CG-5720-11A. This is the reason that the sample search query shown above returns two sets of bam/bai files.

The ability to enter barcodes into the search is planned for a future iteration, feedback from users like you is very helpful for us to properly prioritize this.

  
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