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  • Bowtie2 output options

    Hi guys,

    I have been trying to write unaligned (--un path) and aligned (--al path) reads from a Bowtie2 (Bowtie2 2.0.0-beta7) alignment without success. It is PE 100 bp Illumina exome data. If I run it using the --un-conc and --al-conc option everything works OK. However, I still want the discordant reads to be reported as aligned reads (that's why I do not use the --no-discordant option) and I want those reads which only one mate aligning to be reported as unaligned (thatś why I use the --no-mixed option).
    Is this possible? Any ideas?

    Thanks in advance,

    Fernando

    Parameters:

    bowtie2 -p 6 --phred33 -N 1 -L 30 --no-mixed --un ~/projects/myproject/bowtie/un.fastq --al ~/projects/myproject/bowtie/al.fastq --time --rg-id Flowcell1_Lane3 --rg LB:Lib-bl209 --rg SM:XXXgDNA --rg PL:HiSeq2000 -x $bowtie_reference_dir/genome -1 $raw/XXX_1.fq -2 $raw/XXX_2.fq -S XXX.sam >> XXX.out 2>&1

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