SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
overlapping paired-end reads vs single end reads evakoe Illumina/Solexa 14 07-22-2015 01:35 AM
Overlapping paired end reads in SOAPdenovo Fernando Seixas Bioinformatics 0 11-26-2013 05:40 AM
Overlapping Paired End reads - questions... NRiddiford RNA Sequencing 0 07-19-2012 08:08 AM
Questions about overlapping paired-end reads... FredOnSeq Illumina/Solexa 6 04-18-2011 06:19 PM
How to manage overlapping paired-end reads? FredOnSeq Bioinformatics 2 09-09-2010 02:27 AM

Reply
 
Thread Tools
Old 09-08-2016, 06:32 AM   #1
Patrice
Junior Member
 
Location: Denmark

Join Date: Sep 2016
Posts: 4
Default Collapsed reads vs overlapping paired-end reads !!??

Hello all!


Case:

We did a Sequencing of three yeast strains (not s.cerevisiae) and with reference genome available!

Illumnia MiSeq

around 8,5 million reads each way (paired ends)

most reads around 90-120 bp long

high coverage: around 90x



In the trimming /adapter removal step we saw most of our paired end reads have overlaps



R1 ------------------------->
R2 <-----------------------



99% overlapping paired end reads
1% non-overlapping paired end reads

Question:

Is it better for the next assembly steps (initial contig building, scaffolding)

-> to only use single-end reads:
Collapse the overlapping paired end reads (99 %) into single end reads (since assemblers can have problems with overlapping paired end reads) and use only this single end reads for the assembly (discard the 1%) ?

-> to only use paired-end reads:
use the overlapping paired end reads (99%) and the non-overlapping paired end reads (1%)?

-> to use a mix: single and paired-end reads:
Collapsed into single end reads (99%) and non-overlapping paired end reads (1%).

Thanks
Patrice is offline   Reply With Quote
Old 09-08-2016, 06:58 PM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,696
Default

Cross-posted here.
Brian Bushnell is offline   Reply With Quote
Reply

Tags
assembly, paired-end reads

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 05:25 PM.


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