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Old 01-17-2011, 06:24 AM   #1
emmecola
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Location: ITA

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Default microRNA analysis (no reference genome)

Hi everyone

We performed an RNA-seq experiment using small RNAs in a species with no genome sequence. I've used miRProf to find which microRNAs are expressed in a control sample (3 replicates) and in a stressed sample (3 replicates).

Now I would like to calculate the Fold Change between the two conditions, but I have no idea about the expected inter-replicates variability. Which criteria should I use to filter out expression values with too much difference between the replicates?

Thanks
Moreno
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Old 01-19-2011, 02:15 AM   #2
NicoBxl
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you can use DESes or edgeR , R packages.

There are part of the bioconductor package
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degseq, microrna, microrna sequencing, mirna, rna-seq

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