Sequencing old DNA samples

Question

[priya.bmg]

Hello

I am working with DNA samples which have been extracted like 10-15 yrs ago. We have been facing problems in sequencing these samples with very low yield i.e. low number of hifi reads. We have washed the DNA to remove contamination and tested the DNA quality with gel run, fragment analyser and checked the 260/280 ratios and 230/260 ratios and DNA concentration and it looks perfectly fine. After washing the DNA, we found one sample to be sequenced with good yield, high number of hifi reads. But, another sample failed to run. Has anyone faced this issue

In cases when the number of reads is low, subreads are aligned to hifi reads using tools such as actc from PacBio. Has anyone faced these issues and did you see any other tools to fill the gaps in hifi reads. It would be helpful if some can share their experiences with low yield of hifi reads and solutions used to improve the yield

Thanks

Answer 1

[colindaven]

This is probably best posted to seqanswers.com, that's where I think more biologists are present. This is a bioinformatics site, so members' experience with wet lab questions is likely limited.

I only know that nanopore recommends fresh HMW DNA extractions for their protocols, so this indeed could be a problem.

[priya.bmg]

Thank you. Is there any tool used like actc https://github.com/PacificBiosciences/actc to improve structural variant detection