SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
Index 1 read (i7) - Low Intensity & Low Quality?? EcneuqeS Illumina/Solexa 0 12-11-2018 11:41 PM
bcftools - retain low quality read position support? clintp Bioinformatics 0 05-17-2018 04:42 PM
Transcriptome assembly: Low GC, short contigs, low read alignment jmah Bioinformatics 0 03-15-2017 05:47 PM
Low intensity & quality for Index Read 2 kmcarr Illumina/Solexa 5 09-29-2016 03:16 AM
Low quality in the middle of the read? MG1655 Illumina/Solexa 0 08-12-2012 01:22 PM

Reply
 
Thread Tools
Old 12-12-2018, 02:16 AM   #1
EcneuqeS
Junior Member
 
Location: South Africa

Join Date: Jul 2018
Posts: 2
Default Index 1 read (i7) - Low Intensity & Low Quality??

Good day,

Can anyone advise me on the following regarding a recent amplicon sequencing run on the Illumina MiSeq:

What would be the cause for a relatively low intensity and low quality Index 1 read (i7) compared to Read 1, Index 2 (i5) and Read 2?

The nucleotides at each position within the indices used were balanced.

The run was quite under-clustered.

Also, other than potential dilution problem, what are other reasons for obtaining a significantly higher alignment of Phix compared to what was originally spiked?

Thanks!
EcneuqeS is offline   Reply With Quote
Old 12-12-2018, 06:11 PM   #2
luc
Senior Member
 
Location: US

Join Date: Dec 2010
Posts: 360
Default

Did you use custom sequencing primers for any of the reads?
luc 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 09:08 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO