Is it possible to multiplex a cDNA and gDNA library together in one lane?

[Mabeuf]

Hi

We are running a genomic library on a multiplexed miseq but we have space left for another library and were wondering if it is technically feasible to fill the space with a cDNA library?

I figure that the nucleic content is equivalent but the read structure may bias the samples? but I hope not.

Thanks

[thomasblomquist]

Originally Posted by Mabeuf

Hi

We are running a genomic library on a multiplexed miseq but we have space left for another library and were wondering if it is technically feasible to fill the space with a cDNA library?

I figure that the nucleic content is equivalent but the read structure may bias the samples? but I hope not.

Thanks

This is a research design specific question, and entails understanding whether your library is targeted or not. If targeted, and the gDNA targets are different than the cDNA targets, then yes these can be demultiplexed subsequently. If they are whole genome/transcriptome library preps than a large number of areas will be difficult to discern if they came from the gDNA or cDNA, unless an obvious splice-junction was observed.

I recommend revisiting your library designs to determine if they could be parsed apart computationally. -Tom

[Chipper]

Yes it works fine, assuming of course that they are barcoded.