SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
What insert size for velveth (1.2.10) with 2 sets of reads with diff. insert sizes? Genomics101 Bioinformatics 4 02-07-2014 12:41 PM
BWA insert size calculation in paired end sequencing dg13 Bioinformatics 3 07-30-2013 10:17 PM
de novo sequencing of maize (lane and insert size library) sflong Illumina/Solexa 2 10-31-2011 09:30 AM
insert size question for sequencing xp8 Illumina/Solexa 2 08-25-2011 08:21 AM
short insert size in samll RNA sequencing wangzhijiao Illumina/Solexa 0 07-21-2011 11:37 PM

Reply
 
Thread Tools
Old 06-25-2014, 06:16 PM   #1
seqgirl123
Member
 
Location: U.S

Join Date: Oct 2008
Posts: 76
Default insert size for sequencing

I have a genome library at 350bp. I sequenced it using 2x150bp read length on Miseq v2. Will I miss out on information because the insert size (350bp) is larger than the total sequencing read length (300bp). Should I always make the insert size smaller than the read length? What if I wanted to run a 2x75bp read length , how much will it sequence of the 300bp insert size?
seqgirl123 is offline   Reply With Quote
Old 06-25-2014, 07:36 PM   #2
gaoch
Junior Member
 
Location: china

Join Date: Aug 2013
Posts: 4
Default

The truth is that reads are overlapped, so the missed part of this read pair should be revealed by another one. Besides, a library with insert size of 350bp should have a size around 350, may be 250~450 sometimes. furthermore, sequencing 250 bp insertion with 2*150bp, I would like to say it's a waste of data, cause there are 50 bp is sequence twice.
gaoch is offline   Reply With Quote
Old 06-25-2014, 08:42 PM   #3
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,238
Default

Quote:
Will I miss out on information because the insert size (350bp) is larger than the total sequencing read length (300bp).
It depends on what you are going to use the reads. If you wanted to overlap the paired end reads (R1,R2) to produce longer ones, you will not be able to do it for most of the reads. But, if you are using them to assemble longer contigs most likely it will not make any difference.

Quote:
Should I always make the insert size smaller than the read length?
As explained above if you want to merge read1 and read 2 of fragments you will need to have some overlap in the middle and your insert should be smaller than total cycle numbers.

Quote:
What if I wanted to run a 2x75bp read length , how much will it sequence of the 300bp insert size?
It will sequence 75 bases from either end of insert fragment.
nucacidhunter 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 03:03 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO