Dear community,
we recently sequenced dsDNA fragments by Oxford Nanopore and currently investigate the obtained data. Since our dsDNA fragments are all in the range of 100-3000bp, we wonder if the sequencer favours to sequence smaller fragments more often and thereby introduces a fragment-size dependent bias. Does anybody encountered a similar problem or may even have a test data set that we could use to correct our data with? Ideally Nanopore data from dsDNA fragments in the range of 100-10,000 bp. Any other suggestion is also more than welcome!
Thank you all very much in advance.
Hi, have you found anything yet?
I had the same question and found this recently published article.
https://academic.oup.com/clinchem/article/69/2/168/6794073
It seems to suggest that, if any bias, Nanopore seems to favour long reads over short reads. I wonder if this agrees with your experiments.
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