Sudden intensity jump?

[matth431]

Hi,

Just come in to check on our latest HiScan run and noticed something odd - lanes 3 and 4 had whited (well, greened)-out thumbnails - very bright although occasionally you could make out the pattern of clusters in the background. Lane 5 doesn't seem to suffer from this (still scanning this cycle) and looking at the saved thumbnails neither do lanes 1 and 2. Previous cycles were nothing out of the ordinary.

Checking the intensity plots, I've noticed a sudden jump in intensity for these two lanes, similar to that which occurs ~50 cycles into each read, but the run is currently at cycle 185 (I can see the "planned" intensity jump at cycle 160 as expected).

Has anyone else seen similar issues and are they persistent (i.e. once they occur, do the remaining cycles have this problem or can it be a "bad" cycle which recovers once the reagents are pumped for the next one)? Can the software still call bases with very high intensity?

Thanks,

Matt

[share]

I guess that is not a bubble. I never saw that in our hiseq but we did in ga but not for entire lane only few tiles. Base qualities were bad for these tiles i guess it ll be same in this case to.
The brightness may be due to some sort of precipitation in buffers or mixes. It's a rare event.

[matth431]

I guess that is not a bubble. I never saw that in our hiseq but we did in ga but not for entire lane only few tiles. Base qualities were bad for these tiles i guess it ll be same in this case to.
The brightness may be due to some sort of precipitation in buffers or mixes. It's a rare event.

Coming back to this for anyone who observed a similar problem - we had lane blockages so fluorescence was building up. Eventually, the sequencer gave up scanning those lanes but luckily it was close to the end of read 2 so most of the data was viable.