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RNA-Seq best practice workflow STAR 2-pass mapping question

thkitapcithkitapci Los AngelesMember

Hi,
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) v4.1.2.0
HTSJDK Version: 2.19.0
Picard Version: 2.19.0
STAR: 2.7.1a

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 ?

Thanks
Best Regards
Tevfik Hamdi Kitapci

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