run our pipeline on TCGA data
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7.4 years ago
jonessara770 ▴ 240

Hello all,

I am wondering if it is possible to run our own pipeline (WES, WGS or RNA-Seq) on TCGA raw data without downloading TB of data? do TCGA have fastq/ bam files somewhere that we can login and install our own pipeline and run the TCGA data from scratch...

Thanks sara

NGS • 1.8k views
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Devil is always in the details but take a look at this link for options. Be ready to pay (something) since access is not free AFAIK.

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7.4 years ago
dyollluap ▴ 310

If you have a custom pipeline you would have to download the raw datasets and suffer the costs of storing while processing. There are some commercial vendors (eg 7bridges) offering access to the raw data under the NCI cloud pilot project, however it's limited to a couple of mainstream tools with a simple interface and they will bill you for the compute time. Unfortunately they don't enable direct access to the buckets.

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The Cancer Genomics Cloud (CGC) from SevenBridges allows you to bring your own custom tools/pipeline to the TCGA data using a SDK. In addition, pilot funds from the NCI are available to cover (at least partially) for the compute cost. Direct access to user buckets is also possible via the Volumes API (a more recent feature).

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