One read after the other
bbmap/reformat.sh \
verifyinterleaved=f \
t={threads} \
in={params.fastqs_dir}/{params.sample}.fastq.gz \
out1={params.fastqs_dir}/{params.sample}_1.fastq.gz \
out2={params.fastqs_dir}/{params.sample}_2.fastq.gz
forward and reverse reads are concatenated. Usually, the identifiers of each pair are the same except for a "/1" or "/2".
# forward
zcat {params.fastqs_dir}/{params.sample}.fastq.gz | \
grep '^@{params.sample}.*/1$' -A 3 --no-group-separator | \
pigz -p {threads} > {params.fastqs_dir}/{params.sample}_1.fastq.gz
# reverse
zcat {params.fastqs_dir}/{params.sample}.fastq.gz | \
grep '^@{params.sample}.*/2$' -A 3 --no-group-separator | \
pigz -p {threads} > {params.fastqs_dir}/{params.sample}_2.fastq.gz
####### Gene Expression ####### Splicing
####### Gene Expression ####### Splicing