miRNA-seq data analysis
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just • 0
@just-9837
Last seen 7.0 years ago

I would like to analyze microRNA sequencing data. However I'm lacking the experience here. Which pipeline would you recommend? The idea would be at the end to combine this data with TCGA dataset

Thank you for your help!

miRNA mirna-seq • 4.4k views
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Analyze... to what end? To detect differential expression? To classify samples? To predict binding motifs? Screens?

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Thanks for the reply.

Differential expression will come next. Ideally, it would be nice to have a tool starting from scratches (alignment, quantification etc). Any ideas?

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@lorena-pantano-6001
Last seen 3.9 years ago
Boston

Hi,

Normally you do a first analysis for miRNA annotation and so on ourside R, and then use R and bioconductor packages for differential expression or donwstream analysis.

It's possible you can do all with R, but we use: https://bcbio-nextgen.readthedocs.io/en/latest/contents/pipelines.html#smallrna-seq

For sure you need to spend some time how to use the tools, so nothing that will be running in 5 min.  You will see the main steps and outputs you can have with small RNAseq data.

cheers

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Jon Bråte ▴ 250
@jon-brate-6263
Last seen 2.5 years ago
Norway

This also depends very much on which species you are working on. But check out this recently published online collection of tools. Seems like you can pretty much do the entire pipeline here: http://bioinfo5.ugr.es/srnatoolbox/srnabench/

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