Question: run our pipeline on TCGA data
gravatar for jonessara770
2.6 years ago by
jonessara770150 wrote:

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 • 810 views
ADD COMMENTlink modified 2.6 years ago by dyollluap300 • written 2.6 years ago by jonessara770150

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.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax70k
gravatar for dyollluap
2.6 years ago by
USA, California, Bay Area
dyollluap300 wrote:

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.

ADD COMMENTlink written 2.6 years ago by dyollluap300

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).

ADD REPLYlink written 2.6 years ago by Christian2.8k
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