SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to mix single index and dual index TruSeq libraries pmiguel Illumina/Solexa 31 05-24-2017 03:10 AM
blast WARNING: Failed to access string index ISAM Error code is -12 Zhan yueping Bioinformatics 3 12-15-2014 03:17 AM
Retrieve MiSeq Data still containing index primers etc trasver Illumina/Solexa 3 06-05-2014 05:22 AM
Reproduce genome coverage of ENCODE-CSHL Long RNA-seq data, but failed? josephyan RNA Sequencing 1 10-31-2012 03:51 PM
Failed Index Read - how to restart? coleen_2 Illumina/Solexa 2 02-19-2011 10:57 AM

Reply
 
Thread Tools
Old 04-21-2015, 03:35 AM   #1
dep
Junior Member
 
Location: Russia

Join Date: Apr 2015
Posts: 7
Default Failed second index. Any chances to get some data?

Dear colleagues!
We have conducted a HiSeq 2500 dual index paired end run using TruSeq SBS Kit v3 - HS (200-cycles) chemistry and TruSeq PE Cluster Kit v3 - cBot HS cluster generation kit for libraries prepared with Nextera Rapid Capture Exome. We had 93-8-8-93 cycles, but it seems like we had not enough ICB for the first part of the run due to an error with ICB splitting. So, we have very degraded data for cycles 102-111, including cycles 102-109 for the Index 2 reads. The amount of Q30 nucleotides for Index 2 read is about 0,1%.

Is it worth trying to get any info for the index 2 reads out of such a run to demultiplex the samples?

I believe there are no chances, but I must use any possibility to minimize the losses.
dep is offline   Reply With Quote
Old 04-21-2015, 03:59 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,054
Default

Are you using bcl2fastq for demultiplexing? Have you looked at the "undetermined" pool files to see if the indexes in read 2 have recoverable data (you can overcome one N's in that read but not more).
GenoMax is offline   Reply With Quote
Old 04-22-2015, 06:03 AM   #3
dep
Junior Member
 
Location: Russia

Join Date: Apr 2015
Posts: 7
Default

Thank you for the reply!

Yes, I use bcl2fastq and there are many more Ns in read 2. So, I guess its lost?
dep is offline   Reply With Quote
Old 04-22-2015, 06:22 AM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,054
Default

I was asking about the "tag 2" sequences. They should be present in undetermined file (but concatenated like tag1tag2, 1:N:0:CGACAACCCNNCCC) in the fastq read ID's. You will find the files in Undetermined_indices/Sample_lane* directories.
GenoMax is offline   Reply With Quote
Old 04-22-2015, 07:09 AM   #5
dep
Junior Member
 
Location: Russia

Join Date: Apr 2015
Posts: 7
Default

Yes, I mean the same. Many Ns there.
dep is offline   Reply With Quote
Old 04-22-2015, 07:20 AM   #6
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,054
Default

It is likely that your samples share a common index 2 otherwise you may have been able to get some of them separated based on index 1. Best to write this run off.
GenoMax is offline   Reply With Quote
Old 04-22-2015, 07:23 AM   #7
dep
Junior Member
 
Location: Russia

Join Date: Apr 2015
Posts: 7
Default

OK, thank you for assistance!
dep is offline   Reply With Quote
Reply

Tags
hiseq 2500, illumina, index loss

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 06:01 AM.


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