fastq-mcf: Allow merging multiple FASTQ input files to one (or two in case of paired-end) cleaned fastq file about ea-utils HOT 4 CLOSED

If you have, say, 2 fastq's , you can do this:

rm fif; mkfifo fif;
( gunzip -c fq1.gz >> fif;  gunzip -c fq1.gz >> fif ) &
fastq-mcf adap.txt fif > out

Unlike much bioinformatics software, fastq-mcf is "stream friendly" .... 
meaning it buffers what it needs during initial sampling steps.

Thanks.

Thanks for this very useful tip.

It can also be done without explicitly making named pipes, but by using process 
substitution:
  http://tldp.org/LDP/abs/html/process-sub.html

fastq-mcf \
  -o cleaned.R1.fq.gz \
  -o cleaned.R2.fq.gz \
  adapters.fa \
  <(zcat uncleaned.lane1.R1.fq.gz uncleaned.lane2.R1.fq.gz;) \
  <(zcat uncleaned.lane1.R2.fq.gz uncleaned.lane2.R2.fq.gz;)



fastq-mcf \
  -o cleaned.R1.fq.gz \
  -o cleaned.R2.fq.gz \
  adapters.fa \
  <(gunzip -c uncleaned.lane1.R1.fq.gz uncleaned.lane2.R1.fq.gz;) \
  <(gunzip -c uncleaned.lane1.R2.fq.gz uncleaned.lane2.R2.fq.gz;)


Can this info being added to the wiki?
http://code.google.com/p/ea-utils/wiki/FastqMcf


Thanks

Cool!  I didn't even know how process substitution worked.