Is there a bias after DNA fragmentation? What do you think?

[ecSeq Bioinformatics]

Cutting DNA into small fragments is a key preparation step for DNA sequencing with NGS technology. To reduce errors and increase reliability of the sequence information, every genomic region should be sequenced several times. This means that several copies of a target DNA have to be cutted in different ways to produce overlapping fragments to ensure an good coverage of the whole region of interest. This approach is based on the general idea that genomic DNA break-points are random and sequence-independent.

But there is a problem... read more

[pmiguel]

And your evidence is? Would be helpful if you gave a review of the evidence of the six papers you reference rather than just stating conclusions.

Some DNA damage/modifications could impact the replication of segments of DNA, of course. But it seems like coming up with a way to assay this would be tricky if you want to use sequencing as the assay. For instance, I presume there is some ligation-site bias in library construction that has nothing to do with the fragmentation method per se.

--
Phillip

[ecSeq Bioinformatics]

For instance, I presume there is some ligation-site bias in library construction that has nothing to do with the fragmentation method per se.

--
Phillip

We never claimed that the fragmentation is the only source of biases, did we? But it is a known source and researchers should be aware of it.