What features/analysis should be performed?

[matinnuhamunada]

Would be great if we can list the software or bioinformatic pipelines required for de novo RNAseq analysis.

Pipeline to add:

• [x] FastQC
• [x] MultiQC
• [x] Trimmomatic (already included in Trinity)
• [x] Trinity
• [ ] rnaQuast
• [x] BUSCO - should it be run with rnaQUAST?

[LuthfiNurhidayat]

should we use Trinotate for functional annotation and analysis?

[LuthfiNurhidayat]

should we use this workflow?

[matinnuhamunada]

Is it from this tutorial? https://rnabio.org/module-07-trinotate/0007/02/01/Trinotate/

[LuthfiNurhidayat]

Generally yes, but we made some adjustments since we will do the DE later after biological replicates meet the requirements. So we will do the annotation first and transcript quantification later. And I forget about transdecoder results file is needed to run Trinotate. So we can put Transdecoder before executing Trinotate. Moreover, the Blastp and Blastx results can be optionally used for Trinotate, then we can execute these processes before Trinotate.

[LuthfiNurhidayat]

https://github.com/Trinotate/Trinotate.github.io/wiki