[fanli]

I think low diversity would only cause jaggedness in the intensity profile, but maybe you should check w/ tech support.

Our 16S runs have 1st cycle intensities ~150.

[RickC7]

strange

hi fanli,

hmmm, the run summary you posted on 5-11-2015 shows read 1 intensity at 17 and read 4 intensity at 53. The other run summary from the OP also shows low intensity 1st cycle. This also fits with what I see in 16s libraries on miseq. So, 3 different machines, 3 different places, 3 similarly low 1st cycle intensities...
Tech support is telling me this is the reason I am having issues with run completion. Last 3 runs are terminating randomly, run1- cycle 385, run2-cycle 60, run3 - cycle 587. Tech support has been helpful in replacing kits, but miseq is still out of commission. Have arrange for libraries to be sequenced on another miseq, Qc all checks out so I have little to no concern about the libraries. One comment that came out was " your 1st cycle intensities are very low..." I get a stopped run and funky z-stage errors, z-stage replaced but same issue persists.

[fanli]

My bad - that last screenshot is Called Int. Yeah, you're right - the Cycle 1 intensities for my last run are 30 and 39 for read 1 and read 3, respectively.

We haven't had any issues with runs terminating randomly for 16S libraries though. Although now that I think about it, we did have one bacterial WGS run that died on cycle 515 or so. Something about a .NET framework error and tech support said they hadn't seen it before.

[BioGenomics]

Hi all,

what is the minimum Q-value you would suggest for a 16s read/merged amplicon Trimming/clipping ?

thanks

[thermophile]

I don't trim based on qscore, I use the qscores to merge reads. I use mothur which impliments pandaseq for it's read merging