Illumina Read Stitching

Question

[ManuelDB]

We have implemented the new software provided by Illumina in our mySeq.

The application allows to turn off or on the parametre "Read Stitching". From the Illumina website, I can understand what a stitched read is. However, I have run many samples with both parameters on and off to compare and see differences and both data generated is very very similar.

Can someone explain to me what is this?

Note: What the software explains when clicked in the interrogation mark: When enable, paired-end reads that overlap by 10 or more bases are stitched to form a single read.

Based on this info, I have expected a decent difference in the output but as I said, the data is practically the same. ???

Answer 1

[GenoMax]

Are your reads expected to overlap (for most applications they don't, unless you have short inserts that are smaller than the number of cycles being sequenced)? If they are expected to overlap only then that setting will come into play. If no overlap is expected then that setting rightfully won't make any difference.