SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
23andme raw Illumina intensity reads rworthi Bioinformatics 4 12-01-2011 08:29 PM
Is there any public raw intensity data from RNA-Seq endether Bioinformatics 0 10-10-2011 08:06 AM
First Cycle Intensity Issues jpsmith Illumina/Solexa 1 10-06-2011 12:27 AM
Read Intensity Figure peterbengkui Bioinformatics 2 08-22-2011 08:55 AM
Has Anyone stopped a HiSeq run due to low intensity clusters? ashchin Illumina/Solexa 10 01-25-2011 03:03 PM

Reply
 
Thread Tools
Old 05-27-2008, 04:19 PM   #1
sequencer_lee
Junior Member
 
Location: Washington

Join Date: May 2008
Posts: 9
Default Anyone seen an intensity plot like this?

This is the PhiX lane--anyone seen bases diverge like this? What would cause this? Thanks

sequencer_lee is offline   Reply With Quote
Old 05-27-2008, 04:45 PM   #2
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default

Image comin' up blank for me!
ECO is offline   Reply With Quote
Old 05-27-2008, 05:36 PM   #3
sequencer_lee
Junior Member
 
Location: Washington

Join Date: May 2008
Posts: 9
Default

That's weird--I can see it.
You could try clicking this link:
img144.imageshack.us/img144/734/picture3wz7.png
sequencer_lee is offline   Reply With Quote
Old 05-27-2008, 06:42 PM   #4
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default

Hrm, can see it now.

I haven't looked at enough intensity plots to know.
ECO is offline   Reply With Quote
Old 05-28-2008, 01:15 AM   #5
cgb
Member
 
Location: Cambridge

Join Date: May 2008
Posts: 50
Default

looking in isolation -

looks like you have a very weak chip - or a weakish chip with very high signal loss and you are out of signal by the middle of the read. what is the signal loss rate ?
cgb is offline   Reply With Quote
Old 05-28-2008, 07:30 AM   #6
bioinfosm
Senior Member
 
Location: USA

Join Date: Jan 2008
Posts: 482
Default

Did you use all defaults for the solexa pipeline? Chastity filter of 0.6?
Mid way through the read, there comes a point where A and C, G and T become quite dependent on each other, and the pipeline uses all kinds of matrices to call one from the other.

What is the dna sample, if I may ask!
bioinfosm is offline   Reply With Quote
Old 05-28-2008, 07:50 AM   #7
new300
Member
 
Location: northern hemisphere

Join Date: Mar 2008
Posts: 50
Default

Quote:
Did you use all defaults for the solexa pipeline? Chastity filter of 0.6?
Mid way through the read, there comes a point where A and C, G and T become quite dependent on each other, and the pipeline uses all kinds of matrices to call one from the other.

What is the dna sample, if I may ask!

Huh?

The only corrections the Solexa pipeline performs are crosstalk and phasing corrections. Crosstalk is determined from the first cycle only, and the same matrix is applied to all cycles. The Phasing correction is cycle dependent but is unlikely to cause anything like this.

Would need to see more plots (all intensities/called intensities) in order to figure out what's happening in this case.
new300 is offline   Reply With Quote
Old 07-11-2008, 11:57 AM   #8
sequencer_lee
Junior Member
 
Location: Washington

Join Date: May 2008
Posts: 9
Default

Thanks, guys--the plot was for the PhiX control. Tech support thinks we had a focussing issue. Anyway, it didn't happen on the next run.
sequencer_lee 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 03:40 PM.


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