mirDeep2 edgeR analysis

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Flores Torres, Mariana ▴ 10

@flores-torres-mariana-6100

Last seen 9.6 years ago

Hello, I wondered if anyone has experience with microRNA seq data analysis?? I have miRNA sequencing data from Illumina (control vs treatment) and have used mirdeep2 for analysis (it uses bowtie to aligne to miRBase) but I'm not sure how to perform differential expression, hope someone could please guide me through this! Many thanks! Mariana [[alternative HTML version deleted]]

Sequencing miRNA microRNA Sequencing miRNA microRNA • 3.2k views

ADD COMMENT • link updated 10.7 years ago by Ryan C. Thompson ★ 7.9k • written 10.7 years ago by Flores Torres, Mariana ▴ 10

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hi mariana

i also have to do differential expression for mirna data

i have also used mirdeep2 tool for analysis

could u help me with edger

i have data as follows 2 conditions control vs treated

environment of two genotypes of wheat

i have biological replicates for each sample

my data is as follows:

susceptible
DC1 DC2 DC3
DI1 DI2 DI3 

resistant
CC1 CC2 CC3
CI1(has two runs) CI2 CI3
D-gentype : A B genomes
C- genotype: A B D genomes

i have counts of all my libraries in each condition ready with me as txt files

ADD REPLY • link 7.1 years ago sanjalidhole • 0

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You should probably post a new question instead of adding to a comment to this question (which is almost 4 years old, now).

Before doing that, though, take note of Ryan's answer. You'd do well do try one of the rnaseq analysis toolkits (edgeR or DESeq2) on your miRNA data. I imagine you have a count matrix of miRNAs in rows and samples in columns.

Read through vignettes and user guide's to both packages. Once you have done that, use one of the workflows described there to do your analysis. If you decide to follow up with a new question, please be very specific about what you tried and the steps that are confusing to you so that you can get the best help.

ADD REPLY • link 7.1 years ago Steve Lianoglou ★ 13k

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Ryan C. Thompson ★ 7.9k

@ryan-c-thompson-5618

Last seen 8 months ago

Scripps Research, La Jolla, CA

Hi Mariana, As a first attempt, it would seem that the most straightforward thing to do is to count the reads in each sample mapping to each miRNA and then analyze those counts as you normally would using edgeR. In other words, just treat it like RNA-seq data. If that doesn't work, then you'll need to get more creative, but that should be a good start. -Ryan On Tue 20 Aug 2013 07:01:05 AM PDT, Flores Torres, Mariana wrote: > Hello, > > I wondered if anyone has experience with microRNA seq data analysis?? > I have miRNA sequencing data from Illumina (control vs treatment) and have used mirdeep2 for analysis (it uses bowtie to aligne to miRBase) but I'm not sure how to perform differential expression, hope someone could please guide me through this! > > Many thanks! > > Mariana > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD COMMENT • link 10.7 years ago Ryan C. Thompson ★ 7.9k

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