Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Bowtie Paired-end options days369 Bioinformatics 5 12-12-2012 05:38 PM
Paired End Mapping using Bowtie adarshjose Bioinformatics 8 01-26-2012 08:41 AM
bowtie- paired end - no alignments madsaan Bioinformatics 1 06-27-2011 02:24 PM
bowtie paired end mismatches madsaan Bioinformatics 0 06-22-2011 09:26 AM
Soap2 paired end mode rahul.m.dhodapkar Bioinformatics 1 08-25-2010 08:18 AM

Thread Tools
Old 08-18-2010, 04:19 AM   #1
Senior Member
Location: NL, Leiden

Join Date: Feb 2010
Posts: 245
Default bowtie paired end mode

hi all,

i want to use bowtie for sort of paired end alignment, when i do;


it works fine, and i get two outputs.

However, when i do them in paired end mode;

bowtie.exe TESTTT -1 file1.txt -2 file2.txt

it doesn't work, since it generates no outputs. Someone knows how to generate such a file? Can it be a .fasta file?

boetsie is offline   Reply With Quote
Old 08-18-2010, 05:12 AM   #2
Location: Iowa City, IA

Join Date: Jul 2010
Posts: 95

-f specifies fasta, by default fastq is assumed
adamdeluca is offline   Reply With Quote

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 12:27 PM.

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