SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bowtie2: rRNA data from Silva fail to align with Illumina PE reads jyuems Illumina/Solexa 3 05-07-2014 04:26 AM
Bowtie2 mapping and paired-end reads westeros Bioinformatics 3 03-22-2014 01:02 AM
How to align reads to multiple index in bowtie2 ssharma Bioinformatics 3 07-16-2013 03:13 AM
Using Bfast to align paired end Illumina reads gavin.oliver Bioinformatics 14 01-14-2012 06:51 AM
paired-end reads mapped to genome.. gene with only one direction of paired-end reads? danwiththeplan Bioinformatics 2 09-22-2011 02:06 AM

Reply
 
Thread Tools
Old 06-04-2014, 01:43 PM   #1
sewellh
Member
 
Location: Stanford, CA

Join Date: Jun 2014
Posts: 13
Default Using Bowtie2 for to align paired end reads

Hi all,

Someone in our lab just got finished with sequencing and assembly of a number of contigs. The question was asked, whether or not she found HiSeq to be useful, or if we could use MiSeq in the future.

I thought if I could align the reads onto her contigs, then we could assess the coverage, and possibly whether or not HiSeq was necessary.

I found that Bowtie allows you to align short reads to a reference sequence.

I concatenated the FASTA files for all the contigs and successfully made a bowtie2 index from the file.

Now, I'm trying to map the paired-end reads onto the index:

Code:
./bowtie2 -S -p 2 DscP_kaster -1 KM01_GW1_TAAGGCGA_L005_R1_001.fastq -2 KM01_GW1_TAAGGCGA_L005_R2_001.fastq KM01_bowtie.sam
but keep coming up with the error

Code:
bowtie2-align exited with value 1
What am I doing wrong?
sewellh is offline   Reply With Quote
Old 06-04-2014, 02:08 PM   #2
dbrg77
Junior Member
 
Location: Manchester

Join Date: Sep 2010
Posts: 6
Default

Try change the order of the option -S to the end, immediately before your sam file name, i.e.

do the following:


Quote:
./bowtie2 -p 2 DscP_kaster -1 KM01_GW1_TAAGGCGA_L005_R1_001.fastq -2 KM01_GW1_TAAGGCGA_L005_R2_001.fastq -S KM01_bowtie.sam
dbrg77 is offline   Reply With Quote
Old 06-04-2014, 02:51 PM   #3
sewellh
Member
 
Location: Stanford, CA

Join Date: Jun 2014
Posts: 13
Default

Hmm. I'm still getting the same error. Is there anything I can do to troubleshoot?
sewellh is offline   Reply With Quote
Old 06-04-2014, 03:07 PM   #4
cariboudoug
Member
 
Location: Toronto

Join Date: Oct 2013
Posts: 17
Default

I'm not sure, but do you need to add the "-x" flag indicating an index?

Gavin
cariboudoug is offline   Reply With Quote
Old 06-05-2014, 12:43 AM   #5
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

As Gavin suggested, you need to tell it what index to use:
Code:
bowtie2 -p 2 -x SOMEINDEX -1 KM01_GW1_TAAGGCGA_L005_R1_001.fastq -2 KM01_GW1_TAAGGCGA_L005_R2_001.fastq -S KM01_bowtie.sam
The index files themselves are built with bowtie2-build.
dpryan is offline   Reply With Quote
Old 06-05-2014, 10:50 AM   #6
sewellh
Member
 
Location: Stanford, CA

Join Date: Jun 2014
Posts: 13
Default

That was the problem! Thank you! The tutorials I found said nothing about having the -x
sewellh is offline   Reply With Quote
Reply

Tags
bowtie2, paired end

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 07:33 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO