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#257 Bowtie 2.0.2 corrupt fastq output

pending
nobody
bowtie (175)
5
2012-12-16
2012-11-08
eernst
No

Running bowtie 2.0.2 with the following invocation:

bowtie2 \ --time -p 48 --mm \ --phred33 --sensitive --end-to-end \ -U reads.fastq \ -x ~/data/reference/genome \ --al reads.matched.fastq \ --un reads.unmatched.fastq \ 2> bowtie2.log \ | samtools view -Sb - > reads.mapped.bam

Input reads are long (~500-10000bp).

Both --al and --un fastq outputs are malformed with the seq header occasionally being inserted at the end of the previous read's qual line, rather than on a new line. Also, some quality lines appear to be truncated.

Discussion

  • Ben Langmead
    Ben Langmead
    2012-12-16

    Hi eernst,

    Can you try again with the latest version (2.0.3) and let me know if you still see this behavior? If so, would you mind sharing your data (index and reads) so that I can try to recreate?

    Best,
    Ben

     
  • Ben Langmead
    Ben Langmead
    2012-12-16

    • status: open --> pending