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boutroslab / CRISPRAnalyzeR

CRISPRAnalyzeR: interactive analysis, annotation and documentation of pooled CRISPR screens
GNU General Public License v2.0
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Screens without replicates #32

Closed khayer closed 7 years ago

khayer commented 7 years ago

Hi,

I would really like to use your tool to analyze my first round of samples. I do not have their biological replicates yet and when I tried running the analysis, it failed when trying to run edgeR. Is there a way of selecting only the algorithms that do not require replicates?

Best, Katharina

jwinter6 commented 7 years ago

HI Katharina,

right now this is not possible, at least two samples for either the untreated or treated population is required. Since the analysis of data without any biological replicates at all is not recommended, I only implemented a workaround to allow a single replicate for one of the groups. Unfortunately, this cannot be changed since some degrees of freedom are required.

What can be done (and is often done):

But apart from that I suggest to just be patient until the replicates are there :)

cheers Jan