Hi guys,
I'm performing the RNA sequencing analysis of a set of human samples. Since I'm a newbie of this type of analysis, I followed some published pipelines. Specifically, the pipeline is this one: http://gatkforums.broadinstitute.org/gatk/discussion/3060/how-should-i-pre-process-data-from-multiplexed-sequencing-and-multi-library-designs. Since I only need to measure the gene expression, I don't know if the indel realignment and base recalibration (BQSR) are two necessary steps for my goal. Can you help me to solve my doubts?
Kind regards
B
That is a very good point. If you have time, call mutations for one sample before (i.e. indel realignment and BQSR) and after, and compare the INDELs you are getting.