Poor Nextera XT index read quality on Miseq

[ustar]

Hi everyone,

We are trying to run 12 sample in a Miseq run(PE, dual index), but had some problem with index read2(R3). If we only chose to use single index, then sequencing goes on well.

Cluster(K/mm2) is around 1000 but the R3(index read2) is less than 10 while other Q30 over 70. What is the possible reason? Thanks!

Read1 Read2(index1) Read3(index2) Read4
81.4 87.6 5.4 70.1

[DRYTCYV]

Hi,

Do you know the fragment size?

[Calluna]

My initial thought is that there may not have been enough diversity across reads. What was your indexing scheme? Did you follow the indexing guidelines in the Nextera XT sample prep guide?

See pages 44-46 of user manual C:
http://supportres.illumina.com/docum...15031942_c.pdf