I have a pretty strange problem that I haven't seen discussed here before. I made an amplicon library using the multiplexed primers described on these forums and have begun a single-lane HiSeq run. The resulting amplicons are about 260 bases in length. The run is still in progress (PE-100), but the results from the first read are very weird. The first position of the first read has virtually no sample intensity, although the spiked PhiX shows up nicely. This continues for a position or two, followed by very high intensity from the sample (and the PhiX). The alternating sample intensity continues throughout the first read, but the spiked PhiX stays consistent. The other lanes on the run seem to be fine. What's wrong with my sample?
PS: I'm not doing the sequencing myself (the university core lab is doing it).
-Bryan
PS: I'm not doing the sequencing myself (the university core lab is doing it).
-Bryan
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