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Old 06-20-2016, 06:18 AM   #2
Markiyan
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Location: Cambridge

Join Date: Sep 2010
Posts: 116
Lightbulb As long as the sequencing/index primers are compatible, it is possible to mix.

Dear Lovro,

In principle, as long as the sequencing and index primers are compatible, it is possible to mix libraries in the same lane, but one should be extremely careful with the insert size distribution (make sure there are no small fragments/adapter dimers in any input libs).

Also make sure you allow enough cycles on the index reads (if using 6bp and 8bp indexed reads) use 8 cycles for index.
Demultiplexing can become quite tricky (esp if you have different length indexes), but is doable with manual samplesheet.csv editing.

See the following thread for more info.

http://seqanswers.com/forums/showthread.php?t=26547

I've demultiplexed a couple of runs with Truseq PCR-free + nextera MatePair and a more tricky case of Nextera Shotgun with Nextera MatePair runs.

But if you've got enough samples - do a separate runs if possible - usually it gives better and more consistent performance.
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