Is it OK to multiplex RNA-Seq and ChIP-Seq samples into the same lane? My ChIP is sheared to around 300bp using sonication, and the RNA-Seq samples are fragmented to 300-400bp by cationic RNA fragmentation.
The only problem I can think of is the effect of different-sized fragments on qPCR library estimation (before mixing to multiplex the samples). Are there any other problems I haven't thought of?
The only problem I can think of is the effect of different-sized fragments on qPCR library estimation (before mixing to multiplex the samples). Are there any other problems I haven't thought of?
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