Question: miRNA-seq data analysis
0
gravatar for just
2.4 years ago by
just0
just0 wrote:

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 • 2.0k views
ADD COMMENTlink modified 2.4 years ago by Jon Bråte160 • written 2.4 years ago by just0

Analyze... to what end? To detect differential expression? To classify samples? To predict binding motifs? Screens?

ADD REPLYlink written 2.4 years ago by Aaron Lun24k

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?

ADD REPLYlink written 2.4 years ago by just0
Answer: miRNA-seq data analysis
0
gravatar for Lorena Pantano
2.4 years ago by
Boston
Lorena Pantano90 wrote:

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

ADD COMMENTlink written 2.4 years ago by Lorena Pantano90
Answer: miRNA-seq data analysis
0
gravatar for Jon Bråte
2.4 years ago by
Jon Bråte160
Norway
Jon Bråte160 wrote:

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/

ADD COMMENTlink written 2.4 years ago by Jon Bråte160
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