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Old 10-08-2014, 05:39 PM   #1
Sentinel156
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Location: Melbourne, Australia

Join Date: Oct 2014
Posts: 5
Default cuffmerge samples from different strains or leave separate

Hi,

Possibly a naive question but I am new to RNA-seq analysis. I have RNA-seq (illumina hi-seq 100bp single end) samples from four different yeast strains (one WT, one deletion mutant and the other two are WT but different genetic backgrounds of the same species) with three growth conditions for each strain (12 samples total). I'm currently sequencing the replicates but want to get the analysis method sorted.

When using cuffmerge should I be merging all 12 samples together and then running cuffdiff. Or should I keep some samples separate? Are there advantages or disadvantages to either method?

Thanks in advance.
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