Staggered read pairs
paired read merging
If the paired read length is longer than the biological sequence in the
construct, then the reads overflow into the sequencing primer and adapter
sequences which bind the construct to the flow cell as shown below. I call
this a "staggered" pair.
By default, the fastq_mergepairs command trims
(discards) any "overhangs" at the ends of the reads which do not align to
the other read.
The -fastq_nostagger option causes staggered pairs to
be discarded. This option can be useful when the biological sequence is
known to be longer than the read length, e.g. with 2 x 250 V4 in which case
staggered reads are spurious due to PCR artifacts or other problems. See
also Filtering artifacts by setting a
merge length range.