BBduk in process substitution or with named pipes?

[dietmar13]

hello (brian),

would it be possible to use bbduk as process substituion for mapping, like this.

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)

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...

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

thank you,

dietmar

[dietmar13]

to answer my own question: it works...

it works as follows:

mkfifo pipe1.fq
mkfifo pipe2.fq

bbduk.sh overwrite=true in1=R1_001.fastq.gz in2=R2_001.fastq.gz out1=pipe1.fq out2=pipe2.fq ref=truseq_rna.fa.gz ktrim=r hdist=1 &

( /home/ws/SW_install/bowtie/bowtie-1.1.1/bowtie -q -v 3 -3 0 -p 21 -a -m 100 --sam gencode19 -1 pipe1.fq -2 pipe2.fq | samtools view -Sb - > SID2158.bam ) 2> SID2158.log

rm -f pipe1.fq
rm -f pipe2.fq

dietmar

[Brian Bushnell]

I'm glad you were able to answer that yourself, as I never use named pipes

[dpryan]

Doesn't bash process substitution use named pipes? It ends up that you're using them either way then, it's only a difference of 1 vs. 2 pipes.

[dietmar13]

probably,

but in the first case, bash uses (probably) named pipes internally, in the other case I set and use the named pipes (and i think this is meant with "named pipes" in bash)...

[GenoMax]

@dietmar13: Since you have likely tested this already, does option 1 not work as written or it does?

[dietmar13]

@GenoMax

I didn't try 1 because 2 works. in 1 trimming will be made twice (would be a real waste of resources)...