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How to use GATK for RNA-seq analysis?

danielyindanielyin Posts: 7Member

Hi all:
I find that among all the work flows of GATK
http://www.broadinstitute.org/gatk/guide/topic?name=methods-and-workflows
there are no workflows for RNA-seq analysis.
I understand that GATK mainly focuses on variant calling, can anyone tell me how to use GATK for RNA-seq analysis?

thanks
daniel

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