Question

small RNA Workflow

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4.5 years ago

VineethVenumadhavan ▴ 50

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

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 • 2.1k views

ADD COMMENT • link updated 21 months ago by arun • 0 • written 4.5 years ago by VineethVenumadhavan ▴ 50

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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

ADD REPLY • link 3.5 years ago by weixuchu63 ▴ 10

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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.

ADD REPLY • link 3.5 years ago by GenoMax 147k

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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.

ADD REPLY • link 3.5 years ago by ATpoint 85k

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

ADD REPLY • link 3.5 years ago by weixuchu63 ▴ 10

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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.

ADD REPLY • link 3.5 years ago by weixuchu63 ▴ 10

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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.

ADD REPLY • link 3.5 years ago by VineethVenumadhavan ▴ 50

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

ADD REPLY • link 3.5 years ago by weixuchu63 ▴ 10

score 0 · Answer 1 · 2023-02-21

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.