Grab random subset of FASTQ pairs

paired-fastq-subset.sh

# Staring FASTQ files
export FQ1=1.fq
export FQ2=2.fq

# The names of the random subsets
export FQ1SUBSET=1.rand.fq
export FQ2SUBSET=2.rand.fq

# How many random pairs do we want?
export N=100

# (1) Use paste to merge the two into a single line
# (2) Use awk to "linearize" the two mates into a single record.
#     Add a random number to the front of each line
# (3) Sort by the random number
# (4) Using head, grab the first N (randomly chosen, thanks to the awk above) records
# (5) Use awk to convert back to 2 separate FASTQ files.
paste $FQ1 $FQ2 | \
awk 'BEGIN{srand()}; {OFS="\t"; \
                      getline seqs; getline sep; getline quals; \
                      print rand(),$0,seqs,sep,quals}' | \
sort -k1,1 | \
head -n $N | \
awk '{OFS="\n"; \
      print $2,$4,$6,$8 >> ENVIRON["FQ1SUBSET"]; \
      print $3,$5,$7,$9 >> ENVIRON["FQ2SUBSET"]}'

why do you use export?

just do

blah='asdf'
command "$asdf"

Ha! Good point. It's rote from experience in my "early days".