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Old 07-04-2011, 07:45 AM   #1
Location: Alps

Join Date: Jan 2011
Posts: 27
Question RNA-seq: Replicates, single-end, paired-end story


In my lab they made a first RNA-seq run with single-ends, but because the coverage was a bit low they decided to make a new run on the same samples 6 months later, with the paired-end technology ...
The coverage with the Run #1 is 5-fold lower than with Run #2 (40 million reads). When I plot the 2 runs I obtain a fairly good correlation (r= 0.95).

So now I have the choice to work with the last run (paired-ends) but with NO replicates, or use runs #1 and #2 as replicates but with a mix of the paired-end/single-end technologies. I do not know what is the best solution here - do you have any idea ?

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