pool libraries with and without barcode

[JulienD]

Hey,

Has anyone ever tried to pool two libraries: one with barcode and one without barcode on a MiSeq.
I need to test these two libraries and I wanted to know if we could recover data from the non-barcoded library without problems.
Thanks

Julien

[JackieBadger]

by barcode you mean Illumina index?
And yes... if you demultiplex on the MiSeq it will categorize by index and dump the remainder in an "undetermined" file

[HESmith]

Just be aware that the Undetermined_indices file will also contain some reads from the barcoded sample, due to errors in the index read. Such contamination may or may not be tolerable, depending upon your application.

Harold

[JulienD]

It's perfect, my libraries are coming from 2 different species, so I can discriminate contaminations from the barcoded sample.
Thanks very much for your answer.

Julien