Oxford Nanopore Sequencing Output Related

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3 months ago

Bhavya • 0

Hello

We gave an Oxford Nanopore sequencing run. There it is showing as output that Total Data produced is ~3.3 GB. After that in the output summary window it is showing ~157 MB passed and ~88 Mb failed base call.

So my question is (157 + 88)= 245 Mb of bases passed or failed whatever. So then how is the total data produced is much much higher than this sum? Why is this huge discrepancy?

Please help me to understand why and how it is like that.

Regards
Bhavya

Oxford-Nanopore • 393 views

ADD COMMENT • link updated 3 months ago by Ram 44k • written 3 months ago by Bhavya • 0

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I haven't seen something like that before. It could be that your FASTQ.gz (compressed fastq) are smaller than the total Gbp sequenced, but that discrepancy is too large.

I would re-basecall your data using the current Dorado basecaller and see if it improves.

ADD REPLY • link 3 months ago by colindaven 7.0k

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Is it possible that not all the fast5 files have been basecalled and the 3.3GB was the estimated total data?

ADD REPLY • link 3 months ago by samuel.a.odonnell ▴ 580

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Is this data barcoded? Perhaps you have a large amount of "undetermined" barcode containing sequences?

ADD REPLY • link 3 months ago by GenoMax 147k

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