Using MiSeq with both standard and custom sequencing/index primers at the same time?

[kevin_bryant]

Does anyone have experience performing a MiSeq run using both the standard Illumina sequencing and index primers as well as custom sequencing and index primers at the same time?

If so, how many different custom primers have you successfully used in addition to the standard primers?

Thanks!

[kcchan]

There's really no limit to the number of primers you can mix. Illumina's own primers are a combination of several primers, one for each of their sample prep kits. The only thing is to make sure that your read 1 primers don't accidentally overlap with another library's index primer.