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Question: CRISPR Screens sequence analysis
2
gravatar for falaksher2
2.3 years ago by
falaksher2 • 20
United States
falaksher2 • 20 wrote:

I wonder if Galaxy has support for CRISPR screens e.g. sgRNA sequence analysis pipeline Thanks, Falak
galaxy • 879 views
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 2.3 years ago by falaksher2 • 20
1
gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes. I would suggest trying the Cistrome Project's public Galaxy server. The site has linked publications, example workflows/data, and a google group for direct support.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k
1

Hi, Happy New Year. Thanks for your reply. I think what we mean is to introduce the platforms, such as MAGeCK-VISPR, CRISPRAnalyzeR, and PinAPL-Py, to identify important genes from genome-scale CRISPR-Cas9 knockout screens.

Best wishes,

Mingming

ADD REPLY • link written 10 months ago by mliu63 • 10

Hi Mingming, If the tools/workflows are open source, or an open licence is granted, they could be wrapped for Galaxy. Maybe check in with IUC to see if this is planned? I don't personally know status for more CRISPR-specific tool wrapper dev right now, however, community collab/remote-hack/contributions could be part of this, including your's if interested.

Happy New Year, too :)

ADD REPLY • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks, Jen.

Best wishes,

Mingming

ADD REPLY • link written 10 months ago by mliu63 • 10
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gravatar for mliu63
11 months ago by
mliu63 • 10
mliu63 • 10 wrote:

Highly recommended to set up sgRNA sequence analysis workflow
ADD COMMENT • link written 11 months ago by mliu63 • 10
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