Single read instead of Paired end reads

s_farraj · 10-09-2018, 08:43 AM

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

GenoMax · 10-09-2018, 09:29 AM

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.

s_farraj · 10-09-2018, 09:39 AM

Thanks very much for your useful reply

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10-09-2018, 08:43 AM	#1
s_farraj Junior Member Location: Saudi Arabia Join Date: May 2012 Posts: 7	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

10-09-2018, 09:29 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	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.

10-09-2018, 09:39 AM	#3
s_farraj Junior Member Location: Saudi Arabia Join Date: May 2012 Posts: 7	Thanks very much for your useful reply