small RNA Workflow
0
0
Entering edit mode
16 months ago

Hello World !

Looking forward a solution reagarding choosing best small RNA workflows(pre-processing->results/reports) based on following perspectives

Execution Mode : Linux based, Standalone with command line mode. Not web-based.

Organism : Insects

Based on reviews : mimiARma-Seq | The UEA sRNA Workbench | SePIA | CAP-miRSeq | sRNAbench | QuickMIRSeq | miRge 2.0

Problem : Which one best among workflows listed above / Any better workflows ? Admits each has pros and
cons, but looking forward for a suggestion.

Solution : ?

RNA-Seq miRNA smallRNA • 714 views
0
Entering edit mode

Hello there,

Did you find a solution? I am working on citrus plant sRNA seq data, looking for the best workflows too. I'd like to listen your opinion. Thanks.

Xu

0
Entering edit mode

best is relative, someone else' best may not be so for your data. You may need to try a couple or more workflows. If you are working with a non-model organism (which you are) there are always going to be additional challenges.

0
Entering edit mode

Check out https://github.com/nf-core/smrnaseq which is a nextflow workflow for small RNA-seq. Maybe that is something to take inspiration from.

0
Entering edit mode

Thank you, I will check out it. Do you know The UEA small RNA Workbench?

0
Entering edit mode

Yes, that is very true. Citrus is not a model organism, but we have high quality reference genome. This is my first sRNA seq project, and the published references took different workflows, so I'd like to see some opinion from the experts here. Thanks.

0
Entering edit mode

Hi weixuchu63,

As mentioned by experts here it was hard to choose one and had to arrive in a tailor made solution. FastQC->miRTrace->miRDeep2 is what I have chosen as of now. But continuously looking forward for improvement.

0
Entering edit mode

Which software did you use for alignment? Bowtie or STAR? Thank you.