SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
First Cycle Intensity Issues jpsmith Illumina/Solexa 1 10-06-2011 12:27 AM
Counting reads that jump over a position DerSeb Bioinformatics 0 01-17-2011 06:05 AM
Mosaik Jump database creation freezes Calle Bioinformatics 0 06-23-2010 07:24 AM
mosaik jump database amcrisan Bioinformatics 1 10-23-2009 02:30 PM
Anyone seen an intensity plot like this? sequencer_lee Illumina/Solexa 7 07-11-2008 11:57 AM

Reply
 
Thread Tools
Old 12-26-2012, 12:52 AM   #1
matth431
Member
 
Location: UK

Join Date: Jan 2012
Posts: 36
Default Sudden intensity jump?

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
matth431 is offline   Reply With Quote
Old 01-19-2013, 01:25 AM   #2
share
Member
 
Location: india

Join Date: Mar 2011
Posts: 14
Default

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.
share is offline   Reply With Quote
Old 04-30-2013, 07:05 AM   #3
matth431
Member
 
Location: UK

Join Date: Jan 2012
Posts: 36
Default

Quote:
Originally Posted by share View Post
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.
matth431 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:26 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO