Question: Help with looking at mutations from RNA-SEQ data
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gravatar for ms3389
4.2 years ago by
ms33890
ms33890 wrote:

I have RNASEQ data from from cells that have underwent a knockout treatment using CRISPR-CAS9. I've aligned the data using RUM and did differential expression analysis. Now I want to look at off-target mutations caused by CRISPR and if they can account for the difference in gene expression. How would I go about doing this?

ADD COMMENTlink modified 4.2 years ago by fanli.gcb690 • written 4.2 years ago by ms33890
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gravatar for fanli.gcb
4.2 years ago by
fanli.gcb690
Los Angeles, CA
fanli.gcb690 wrote:

For calling variants, try: http://gatkforums.broadinstitute.org/wdl/discussion/3892/the-gatk-best-practices-for-variant-calling-on-rnaseq-in-full-detail

Then your typical eQTL analysis...?

ADD COMMENTlink written 4.2 years ago by fanli.gcb690

A nice introduction to "typical" eQTL analysis E-Book

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by H.Hasani900
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