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Old 02-14-2012, 11:12 AM   #1
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Location: CA

Join Date: Feb 2012
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Default Bowtie2 --al and --un: no output

Hi everyone,

I'm trying to align a set of paired-end reads from 75-750 bp in length with bowtie2. My previous workflow used bowtie1 and relied on the --un and --al flags to filter reads. So, when the latest bowtie2 beta added support for these flags, I decided to try it out.

Unfortunately, when I use these flags with bowtie2, I do not get any output. That is, if the flag is --un <filename>.fastq, the program creates the file <filename>.fastq but without any data inside (filesize = 0). I was expecting something along the lines of the bowtie1 output, i.e. --un <filename>.fastq creates files <filename>_1.fastq and <filename>_2.fastq. That is not the case, however, and I was wondering if anyone was experiencing the same problems or had found a solution. By the way, the same behavior results when I use the --al flag as well.

This is the version information from my OS X 10.7.2 installation
> bowtie2 --version
/usr/local/bin/bowtie2-align version 2.0.0-beta5
Compiler: gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.1.00)
Options: -O3 -m64 -msse2 -funroll-loops -g3
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

I also ran the same commands on a 64-bit Ubuntu 11.10 installation and the behavior was no different. Unless the --al and --un flags actually don't work, I'm at a loss to explain what's happening. Any ideas?
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Old 02-14-2012, 12:04 PM   #2
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Location: MA

Join Date: Oct 2010
Posts: 160


I've not working too much with bowtie2, so I decided to test it and see what happens. This is my version (linux):
version 2.0.0-beta5
Built on compute-0-38.local
Thu Dec 15 01:02:29 EST 2011
Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)

My first surprise was the the reference needs to be indexed with the own bowtie2-build (doesn't work with my previous index of bowtie1). But the options --un and --al seems to work. Could you place the exact commands you're using? At the ubuntu installation, do you get any info on the terminal why isn't working?
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Old 02-14-2012, 12:41 PM   #3
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Aren't you supposed to use --un-conc for paired-end reads? (which would be equivalent to the old --un) I just started using this today and it seems to work.
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Old 02-14-2012, 01:08 PM   #4
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I just tried the --un-conc and --al-conc and now it's working. The output file is named a little differently, but at least the reads are being written. Now I just need to tweak the rest of the parameters...

Thanks for your help!
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