Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Miseq Paired-End Cluster Identification retroant Illumina/Solexa 4 10-19-2012 04:55 AM
How to Demultiplex a Nextera paired-end MiSeq run allo Illumina/Solexa 6 02-27-2012 08:10 AM
paired-end reads mapped to genome.. gene with only one direction of paired-end reads? danwiththeplan Bioinformatics 2 09-22-2011 03:06 AM
Bowtie Illumina paired end reads alignment empyrean Bioinformatics 3 09-20-2011 10:51 AM
BWA alignment for paired end reads AvinashP Genomic Resequencing 2 06-08-2010 04:11 AM

Thread Tools
Old 12-06-2012, 07:58 PM   #1
Location: EU

Join Date: Sep 2010
Posts: 52
Default 250bp paired end Miseq reads alignment

Hello all

Recently we upgraded our miseq and got 2*250 run data. Does anyone have experience in aligning this sort of data? I have been using bwa till now for previous runs when it produced 2*150. Unable use bwa on this data using Bwasw as it didnot support paired end data. I am looking in to bowtie2 now to use as aligner. My references are amplicons and the size is approximately 2kb. In bowtie2, they are suggesting to use bowtie2 for longer genomes. Any thoughts on this?
empyrean is offline   Reply With Quote
Old 12-07-2012, 08:33 AM   #2
Senior Member
Location: Boston area

Join Date: Nov 2007
Posts: 747

One approach would be to use a tool such as FLASH to merge many of your read pairs into single reads, then align those long reads with bwasw.

Of course, for what doesn't merge you still have the old problem. But for very long reads, and especially matching to a small target genome (amplicons), I'm wondering if just aligning them independently with bwasw will work just fine. Paired-end alignment is convenient and may give better specificity in some cases, but a large fraction of the time, particularly with a small genome, it isn't actually gaining anything. Of course, you will lose the convenient auto-generation of insert size information, and some sort of post-processing would be needed if you require that.
krobison is offline   Reply With Quote
Old 12-07-2012, 08:42 AM   #3
Senior Member
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 380

you can use Bowtie/Bowtie2...BLAT...BFAST
JackieBadger is offline   Reply With Quote
Old 12-12-2012, 01:36 PM   #4
Location: SW UK

Join Date: Nov 2011
Posts: 83

The following paper suggests that bowtie2 offers a marginal advantage over bwasw when it comes to aligning 2x250 versus 2x150. They did use simulated data however, but worth experimenting with.
swNGS is offline   Reply With Quote

bowtie2 bowtie

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 10:59 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO