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RNA-Seq best practice workflow STAR 2-pass mapping question
I want to use RNA-seq best practice workflow (https://software.broadinstitute.org/gatk/documentation/article.php?id=3891)
I have a couple of questions:
1) This workflow was last updated on 2017 is this still the current suggested workflow ?
2) I have the following software versions installed
The Genome Analysis Toolkit (GATK) v188.8.131.52
HTSJDK Version: 2.19.0
Picard Version: 2.19.0
Are these the right versions for this workflow ?
3) STAR has a parameter called --twopassMode It seems this is not used in the GATK workflow. Do you have any comments on this ? Should I use this mode or just stick to the method described in the workflow ?
Tevfik Hamdi Kitapci