Concerns for combining data from HiSeq 2000 and HiSeq 2500

[jaaker]

What are the concerns of combining data that was run on a HiSeq 2000 and HiSeq 2500? We ran several samples 6 months ago on a HiSeq 2000 (one per lane, single-end). Our Sequencing Core recently upgraded their machines to HiSeq 2500. If we run other samples on the HiSeq 2500, how comparable is the data to that generated on HiSeq 2000? We use Bowtie, TopHat, DESeq as our pipeline after it comes off the HiSeq.

Any help would be greatly appreciated.

-Josh

[kcchan]

There shouldn't be any differences between the HiSeq 2000 and HiSeq 2500 in high output mode. The only change is the addition of the 2 lane rapid run mode, which may have different results due to the differences in read depth per lane.