small RNA Workflow

Question

[VineethVenumadhavan]

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 : ?

[weixuchu63]

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

[GenoMax]

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.

[ATpoint]

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.

[weixuchu63]

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

[weixuchu63]

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.

[VineethVenumadhavan]

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.

[weixuchu63]

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

Answer 1

[arun]

Hi all,

If you have database available for a non-model organism from either miRBase or MirGeneDB, I can help you build custom libraries to map and quantify the miRNAs. I am currently maintaining miRge3.0, and I can help you with specific queries. You can always test it out which should also help the community. The best way to reach out is to create an issue here https://github.com/mhalushka/miRge3.0. I will try to get back at the earliest.