Help with looking at mutations from RNA-SEQ data

Question

[ms3389]

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?

Answer 1

[fanli.gcb]

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...?

[H.Hasani]

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