Support #24
Setting up the NGI-RNAseq pipeline on UCT Hex
Description
Katie received a support request to analyse human RNA-Seq data. We do not have a pipeline ready for just pushing RNA-Seq data through.
We have also seen in the CBIO 2017 bioinformatics needs survey that there are many users interested in RNA-Seq analysis.
To get ready for the Katie's analysis and also doing planning ahead we need to start setting up a portable/robust RNA-Seq pipeline that initially does analysis on human data only. We can look into existing pipelines or develop our own.
Existing pipelines that might get things done
- https://github.com/SciLifeLab/NGI-RNAseq/ is developed by a bioinformatician that is very active in the Nextflow community. Jon had a look at the pipeline and said it is worth getting it up and running.
- Jenny Drnevich mentioned that they have a Nextflow pipeline based on the new version of the H3ABioNet RNA-Seq SOP. Might also be worth looking into that. Gerrit can follow up on this.
For now Katie is setting up the NGI-RNAseq pipeline on UCT Hex and will check if we can just use the pipeline as is.
Subtasks
History
Updated by Gerrit Botha about 7 years ago
Katie I've talked to Chris Fields he is working with Jenny. He will check if he can make their pipeline available. He says it is basically a template from the one that you are currently working but expanded to include Salmon counts and more QC. If he shares the code we can see what he means.