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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
64-bit
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?
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
64-bit
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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