#288 unaligned reads to fastq: --un and --no-unal conflict is back in ver 2.1.0


I noted in bug ticket #205 that this issue was fixed for release 2.0.7; but it seems to be present in release 2.1.0.

I use --un flag to capture unaligned reads to a fastq file for a subsequent alignment step. When I add --no-unal to drop those same unaligned reads from the SAM output, then they also don't get written to the unaligned fastq file (the file gets created, but no records get written).

Command line that causes the bug:
bowtie2 -q --phred33-quals --very-sensitive -k 10 --un PL02.not.genomic.fastq --no-unal --threads 4 -x Pf.genomic_idx -U PL02.not.ribo.fastq 2> PL02.Bowtie2.AlignMetrics.txt | samtools view -bS -o PL02.genomic.bam -


  • Val

    Val - 2013-07-29
    • assigned_to: Val
    • Priority: 5 --> 2
  • Val

    Val - 2013-07-29

    Hi Bob,

    Thank you for letting us know about this problem. We will look into this for the next release.

  • skatzman

    skatzman - 2013-11-14

    This sounds like the same problem that I described in this bug ticket:

    279 Bowtie2 2.1.0 missing unmapped reads for --un-conc

  • Val

    Val - 2014-02-28

    Fixed in 2.2.1

  • Val

    Val - 2014-02-28
    • status: open --> closed

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