SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Trimmomatic and Multiplexed Samples cbaudo Bioinformatics 5 02-20-2015 07:54 AM
Read number variation in pooled/multiplexed samples -- any tips? gringer Illumina/Solexa 2 01-06-2012 12:18 PM
Generating base quality information after sequence improvement KanyeDidIt Bioinformatics 5 02-24-2011 09:28 AM
Alignment of multiplexed fragment samples (SOLiD) NGS-Jo Bioinformatics 0 01-25-2011 02:36 AM
Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples Asashoryu Literature Watch 0 11-04-2010 01:55 PM

Reply
 
Thread Tools
Old 09-28-2015, 08:11 AM   #1
sridharacharya
Member
 
Location: Institute, WV

Join Date: May 2010
Posts: 24
Lightbulb correlation in per base sequence quality profiles of multiplexed samples.

I have a question related to the "per base sequence quality" profiles.
In a Illumina HiSeq 150bp paired end runs of multiplexed samples, I found that the "per base mean sequence quality" profiles of all the samples correlate with each other. Please see the attached file for figures of quality profiles of all samples, for forward(read1) and reverse (read2) reads.

Though the variation in quality is very small (within 1 quality score), I was expecting that the variation should be rather random for each sample. Is this normal and a common occurrence, and a characteristic of the machine, with something to do with the base calling at each cycle?

* There is a prominent dip in quality at around 105 position in both forward and reverse reads. I was advised by the Sequencing provider that this is a common occurrence, associated with an increase in the laser intensity which occurs around this position. Is it true for all HiSeq runs?

Thanks for your suggestions.
Attached Files
File Type: pdf PBSQ.pdf (265.7 KB, 6 views)

Last edited by sridharacharya; 09-28-2015 at 08:18 AM.
sridharacharya is offline   Reply With Quote
Old 09-28-2015, 08:18 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,087
Default

@sridhar: I moved this post to a new thread since it is not directly related to FastQC.
GenoMax is offline   Reply With Quote
Old 09-28-2015, 08:46 AM   #3
sridharacharya
Member
 
Location: Institute, WV

Join Date: May 2010
Posts: 24
Default

Thanks @GenoMax, could you quickly point me how to start a new thread ? I could find buttons/links, to send replies, but not start a new thread.
sridharacharya is offline   Reply With Quote
Old 09-28-2015, 08:49 AM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,087
Default

Quote:
Originally Posted by sridharacharya View Post
Thanks @GenoMax, could you quickly point me how to start a new thread ? I could find buttons/links, to send replies, but not start a new thread.
SeqAnswers.com --> Forums (left nav pane) --> Select Sub-Forum --> "New Thread" button at the top left of page.
GenoMax 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 11:12 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO