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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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10x sc rna-seq support in bcbio #1986

Closed apastore closed 5 years ago

apastore commented 7 years ago

Hi Brad, Hi Rorky, I was wodering are planing to add 10x to the supported Platform for scRNA-Seq?

Thanks! Alessandro

roryk commented 7 years ago

Hi Alessandro,

Yes-- I just need the list of possible cellular barcodes from 10x and we can add support for it.

apastore commented 7 years ago

Thanks! I will inquire 10x for this if anybody already have a list available.

That's amazing ! Alessandro

Sent from my iPhone

On Jun 24, 2017, at 3:45 PM, Rory Kirchner notifications@github.com wrote:

Hi Alessandro,

Yes-- I just need the list of possible cellular barcodes from 10x and we can add support for it.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

ro6ert commented 6 years ago

Hello Rory,

I was wondering if this is available in a development branch. I didn't see 10x among the bcbio/data/ directory.

Thankyou for all your work on this pipeline.

Best, -Rob

mjsteinbaugh commented 6 years ago

Hi @ro6ert, we're still testing 10X Chromium barcode support, but this is planned on being added in a future release. In the meantime, you can use cellranger to generate the counts. I've been using that along with our bcbioSingleCell R package (see readCellRanger() function) to load up 10X data and run QC/clustering.

roryk commented 5 years ago

Thanks-- cellranger is really easy to run, and bcbio isn't doing anything super special with 10x support, so we've defaulting to running cellranger for 10x data and working downstream from that. We are planning on improving single-cell and may end up adding 10x support as part of that, but for now I'd just stick with what we do: run cellranger.