Insert size 350bp vs 400bp, any major downstream difference?

Question

[serpalma.v]

Hello!

I have two data sets one from HiSeq4000 with an insert size of 350bp and another set of reads from NovaSeq with average 400bp. I am wondering if I should have any reasons to belive there would be major consequences of this difference down the line.

Both sets of reads have the same length (150bp).

[GenoMax]

Without completely knowing what you are doing I would say there shouldn't be a major consequence. There is generally a distribution of inserts anyway so the two insert size distributions should overlap to an extent.

[serpalma.v]

I also though so too, I am doing SNP discovery