SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
Understanding Read Groups for single end and paired end data imsharmanitin Bioinformatics 1 07-10-2018 03:05 AM
Retrieving single and reads from paired end read sequencing run Kaizen Bioinformatics 3 09-09-2016 06:38 PM
Single end read with paired end reads tahamasoodi Bioinformatics 2 01-16-2016 07:46 AM
Mixing paired-end and single-end reads in Tophat: Do I have to reverse the SE-reads f JonB Bioinformatics 5 12-11-2015 01:08 AM
Confusion about single end vs paired end read output on Illumina HiSeq acidcoated Illumina/Solexa 1 03-19-2015 08:56 AM

Reply
 
Thread Tools
Old 10-09-2018, 07:43 AM   #1
s_farraj
Junior Member
 
Location: Saudi Arabia

Join Date: May 2012
Posts: 5
Default Single read instead of Paired end reads

Hi all,‎
I want to use 300 cycle reagent kit from illumina with MiSeq
So, My questions are:‎
‎- Can I choose single read from Illumina Experiment Manager and read 300 bases from one ‎direction instead of 150 from each side in Paired end read situation?‎
‎-Is there any negative effect on reads if I did that? like the quality will be low at the last 50 or ‎‎100 bases of the read for example.‎
‎-Doing that doesn't have any relation with using dual-indexing, am I right? ‎
I hope my questions are clear and I get a reply from anyone of you.‎
Many Thanks
Suha
s_farraj is offline   Reply With Quote
Old 10-09-2018, 08:29 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,795
Default

1. Yes (AFAIK).
2. Quality will be lower for the last set of cycles. Depending on your library quality (and nucloetide diversity) that effect may be more or less pronounced.
3. Index reads are separate from main reads. If you are asking if a 300 cycle kit could be run as 300 SE x 7 X 7, then yes.
GenoMax is offline   Reply With Quote
Old 10-09-2018, 08:39 AM   #3
s_farraj
Junior Member
 
Location: Saudi Arabia

Join Date: May 2012
Posts: 5
Default

Thanks very much for your useful reply
s_farraj 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 05:54 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO