Rebecca Eliscu

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3. TCGA RNA-Seq counts workflow -- fails for all or most samples

Hi Jason, Is there a fix I can implement for this? And how might I go about tracking down the authors of this workflow? Thanks, Rebecca

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• November 02, 2020 20:16
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3. TCGA RNA-Seq counts workflow -- fails for all or most samples

Hi Jason, Apologies, I thought I successfully added the user earlier. Link to workspace: https://app.terra.bio/#workspaces/thisnameistotallyunique/TCGA_LGG_hg38_OpenAccess_GDCDR-12-0_DATA%20copy

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• Edited September 28, 2020 17:16
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3. TCGA RNA-Seq counts workflow -- fails for all or most samples

Hi Jason, thanks for your response. I shared the workspace, as instructed.  These are the relevant submission IDs for the 'gdc_file_downloader__RNAseq__HTSeqCounts__gene_expression_quantification__...

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• September 27, 2020 22:19
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TCGA RNA-Seq counts workflow -- fails for all or most samples

I've run the 'gdc_file_downloader__RNAseq__HTSeqCounts__gene_expression_quantification__txt__cfg' workflow several times on the 1015 samples available in the "TCGA Brain Lower Grade Glioma Open-Acc...

• Rebecca Eliscu
• September 25, 2020 00:52
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3. How can I get TCGA data into the notebooks for analysis?

This has been very helpful -- thank you!

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• September 21, 2020 20:52
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3. How can I get TCGA data into the notebooks for analysis?

Hi Samantha,  Thanks again. The output of the workflow (gdc_file_downloader__WXS__SomSnipAggrMask__masked_somatic_mutation__maf__cfg) is MAF files for 1015 samples. As such, to do any analysis on t...

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• September 18, 2020 20:58
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3. How can I get TCGA data into the notebooks for analysis?

Hi Samantha, thanks for your response.   Having run a workflow, I see each sample's output is buried deep within it's own sub directory path in my workspace bucket, so I have a couple questions abo...

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• September 17, 2020 20:41
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3. Analyzing TCGA Data on Terra

I would echo this question.

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• September 16, 2020 18:29
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