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

Similar Threads
Thread Thread Starter Forum Replies Last Post
MiSeq v3 600 Run Stopped at 301 cycle rahulrahi24 Illumina/Solexa 3 02-13-2017 05:16 AM
Illumina MiSeq 16S run quality MiSeqUserLUX Metagenomics 19 11-18-2016 07:19 AM
Total reads from MiSeq 16S V4 PE run Egansbay Illumina/Solexa 8 03-03-2016 07:04 AM
16S Miseq run with 96 indexed samples marcpavi Illumina/Solexa 7 09-26-2015 01:15 AM
Cleaning amplicons before Nextera + Miseq run?? SDK Illumina/Solexa 3 02-14-2014 04:43 AM

Thread Tools
Old 10-13-2018, 08:22 AM   #1
Location: Greece

Join Date: Jan 2014
Posts: 75
Default Share run between NEBNext smallRNA and 16s amplicons in v3-600 MiSeq run?

Hi all,
for testing purposes we are thinking to put a small amount (~2-3 %) of a smallRNA library (NEBNext) in a run that will otherwise consists only of 16s amplicons (~490 bp, Nextera-type 8 bp dual indexes). Would this be likely to cause any problems? Obviously the size of the amplicons is much bigger, so the clustering efficiency might be very different, but by adding such a small amount I don't think it should be a problem. I looks to me like the NEBNext kit uses the TruSeq sequencing and index primers, so we would get both a forward and reverse read of the smallRNA, along with a "fake" index i5.
Edit: Correction, the index read (i7) and reverse read would be using the TruSeq primers, but for the forward miRNA read it would use another primer; I can't figure out which from the information available from Illumina. I suppose it is in there in the HP10 primer mix.

If everything looks OK from the testrun, the plan is to do a v3-600 run of the smallRNA library, but with a long since expired sequencing kit, and using less than the available 600 cycles. We hope the quality will be sufficient for the few cycles we need even from a very much expired kit.

Last edited by JBKri; 10-15-2018 at 01:37 AM. Reason: corrections
JBKri is offline   Reply With Quote
Old 10-13-2018, 10:05 AM   #2
Senior Member
Location: US

Join Date: Dec 2010
Posts: 446

As long as the short library molecules are a smaller fraction of the loaded libraries (<20%?) there will be no problem.
luc is offline   Reply With Quote
Old 10-16-2018, 12:04 PM   #3
Senior Member
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,317

I agree, it will probably work fine for you.
pmiguel is offline   Reply With Quote

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 08:55 PM.

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