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Help with looking at mutations from RNA-SEQ data

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?

rna-seq next-gen alignment sequence snp
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updated by fanli.gcb fanli.gcb • written by ms3389 • ms3389

2 answers

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written by thunth4 • thunth4

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...?

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written by fanli.gcb fanli.gcb

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

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written by H.Hasani H.Hasani

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