Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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) v220.127.116.11
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