Can I load two DNA and two RNA samples to one HiSeq 2500 rapid mode flowcell?

[ymc]

Is it technically possible? Or do I need to put them in two rapid mode flowcells?

Thanks in advance.

[kwaraska]

As long as the read type (single/Paired) and base length is the same, it doesn't matter what sample type is in any given lane.

The only time it matters is in the processing what you align it to-genome or transcriptome.

[ymc]

Yeah. That's what I thought. But a BGI staff told me that's not possible. Can it be due to different library sizes?

[kwaraska]

It would be a problem to combine them into one lane as different sizes as they would not cluster equivalently, but separate lanes should be fine.

[SNPsaurus]

Are the sequencing primers for the two libraries the same?

[ymc]

It would be a problem to combine them into one lane as different sizes as they would not cluster equivalently, but separate lanes should be fine.

Thank you for your reply. Two of them are exome and the other two are rna-seq. I presume these two sets are prepared differently but they should be at least be able to fit in two lanes. Let me call them and check again...

[weigrc]

Since there are two lanes per Rapid Run Mode flow cell, you may can try to load each type of library into each flow cell lane independently.

http://www.illumina.com/products/truseq_rapid_duo_cbot_sample_loading_kit.ilmn

[ymc]

I called BGI again. They said it is actually feasible but they haven't had any experience with the Truseq Duo Loading Kit yet, so that's why the rep answered that way.

I consider my problem as solved. Thanks everyone for contributing.