I received 150bp SE Nextseq Fastq files from two similar experiments. Reads from one experiment are structured: 5' primer -- DNA -- 3' primer -- indexed adapter (partial - no index). Reads from the second experiment are structured: DNA-- 3' primer -- indexed adapter (almost complete - index included).
The reads of the first experiment are useless as they do not contain the index within the adapter. What controls the location of the "limited view window" within the sequence?