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Should one combine normalization methods in RNA-seq? BGould Bioinformatics 2 07-20-2016 11:32 AM
Should I combine RNA-Seq results from two sequencings szy0931 Bioinformatics 0 06-09-2016 08:12 PM
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Old 06-10-2016, 01:38 PM   #1
szy0931
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Default Should I combine RNA-Seq results from two sequencings

I am doing bacteria RNA-Seq with Illumina HiSeq.
I did the experiment twice with the same strains.
Each experiment has 3 biological replicates for each strain.
Now I have results from the two experiment.
Should I combine the results for analysis from the step of Cuffmerge?
Thank you!
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Old 07-20-2016, 07:16 AM   #2
bastianwur
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You have the same experiment twice?
To what do you want to compare it to?
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Old 07-20-2016, 07:19 AM   #3
Macspider
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Before merging them I would go with some statistical test to see their closeness. For example, run cufflinks on both separately and then do a principal component analysis (PCA) with R to see how close the results are.

But first: why do you say that they are two experiments with 3 replicates each? Does this mean that they are two different conditions? In that case, if you merge them you lose information, unless you want to do a gene prediction and thus you need all in one file.
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