hello (brian),
would it be possible to use bbduk as process substituion for mapping, like this.
i do not want keep the trimmed fastq-files, but have to ensure pairdness. how can i repress the output of the each other read?
or would it even work somehow with named pipes...
thank you,
dietmar
would it be possible to use bbduk as process substituion for mapping, like this.
Code:
mapper read1 <(bbduk.sh in1=R1.fastq.gz in2=R2.fastq.gz out1=stdout.fq out2=NULL ref=ref.fa.gz ktrim=r hdist=1) read2 <(bbduk.sh in1=R1.fastq.gz in2=R2.fastq.gz out1=NULL out2=stdout.fq ref=ref.fa.gz ktrim=r hdist=1)
or would it even work somehow with named pipes...
Code:
mkfifo pipe1.fq mkfifo pipe2.fq bbduk.sh in1=R1.fq.gz in2=R2.fq.gz out1=pipe1.fq out2=pipe2.fq ref=ref.fa.gz ktrim=r hdist=1 mapper read1 <pipe1.fq read2 <pipe2.fq
dietmar
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