problem in illumina samples

[anurupa]

hi
i have 2 samples(replicates) that are supposed to be run on a illumina machine for paired end sequencing. but unfortunately i found 1 replicate is bad interms of quality. can i use replicate2 alone? but will it nt effect the read number? by putting the more sample in the lane will it increase the number of reads?

[JPC]

If you add as much library for sample 1 as you were intending on doing for samples 1 and 2 then yes you will get more reads for sample1. When you set up the run you won't need to read the barcode.

The only problem with loading one sample is if it is 'low complexity', in that case you can spike it with phiX to ensure sufficient diversity.