HiSeq Vs MiSeq

[RajaRaghu]

Hi all,
We constructed a library, using 140-160bp cut fragment as recommended by illumina. We did a 1X50bp run. We compared it with HiSeq data we obtained earlier.
1. In all cases, the HiSeq is producing a higher number of 21nt than 24nt but the reverse is true for the MiSeq run. Is there any technical reason for this bias?
2. We observe a peak at 32-33nt in the MiSeq. what it represents? Any suggestions?

Thanks for your reply.

[pmiguel]

I can't think of a reason to think the instruments are responsible for this. Seems far more likely that library construction for the previous HiSeq data differed from that for your MiSeq run.

--
Phillip

[RajaRaghu]

Thanks Phillip.
We also came to the same conclusion.