Question: CRISPR Screens sequence analysis
2
gravatar for falaksher2
17 months ago by
falaksher220
United States
falaksher220 wrote:

I wonder if Galaxy has support for CRISPR screens e.g. sgRNA sequence analysis pipeline Thanks, Falak

galaxy • 387 views
ADD COMMENTlink modified 19 days ago by Jennifer Hillman Jackson23k • written 17 months ago by falaksher220
1
gravatar for Jennifer Hillman Jackson
19 days ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 19 days ago by Jennifer Hillman Jackson23k
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 REPLYlink written 14 days ago by mliu6310

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 REPLYlink written 14 days ago by Jennifer Hillman Jackson23k

Thanks, Jen.

Best wishes,

Mingming

ADD REPLYlink written 14 days ago by mliu6310
0
gravatar for mliu63
21 days ago by
mliu6310
mliu6310 wrote:

Highly recommended to set up sgRNA sequence analysis workflow

ADD COMMENTlink written 21 days ago by mliu6310
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