I'm currently working with DNA samples originating from museum specimens, this means they have been stored in formaldehyde for the last 50-100 years.
The DNA I'm analysing has been sequenced by Illumina NovaSeq 6000 with paired-end sequencing.
As far as I'm aware NovaSeq uses two-colour chemistry, where Green is T, red is C, yellow (green + red) is A, and no green, no red is G. Over time and increase in sequencing cycles the green and red signal will become weaker, resulting in mistaken categorization of the nucleotides as G in the tails of reads.
This poly-G pattern is however only observed in the 3' end of the 2nd read in the pairs, which I find a bit weird.
Is this an expected pattern (only in the 2nd read in a pair) from NovaSeq or could this possibly also have something to do with my samples being stored in formaldehyde for the last 100 years, thus degrading or affecting the DNA?