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Forum: Oxford Nanopore Yesterday, 02:42 AM
Replies: 1
Views: 579
Posted By gringer
Well, there's the official ONT protocol which...

Well, there's the official ONT protocol which requires special tips and very careful standard plunge pipetting in order to not damage pores, and there's the negative-pressure gentle loading protocol...
Forum: Oxford Nanopore Yesterday, 02:37 AM
Replies: 1
Views: 606
Posted By gringer
I assume you mean Mk1b; the Mk1c is a single...

I assume you mean Mk1b; the Mk1c is a single enclosed unit, including sequencer, screen, and computer.

There are two must-haves for a MinION sequencing computer: an NVIDIA GPU graphics card, and...
Forum: Sample Prep / Library Generation 04-14-2022, 04:17 AM
Replies: 5
Views: 915
Posted By gringer
Literature? I don't understand what you mean by...

Literature? I don't understand what you mean by that.

I've noticed across many different runs that sequencing run performance on nanopore for the same prepared and adapted library has...
Forum: RNA Sequencing 04-11-2022, 12:18 PM
Replies: 1
Views: 1,031
Posted By gringer
You haven't given enough information about the...

You haven't given enough information about the NovaSeq runs. What chip? What read length? Paired end?

Are you paying the same amount for ONT as for NovaSeq? If so, you'd likely be using PromethION...
Forum: Sample Prep / Library Generation 04-11-2022, 12:05 PM
Replies: 5
Views: 915
Posted By gringer
Assuming you're doing this on a MinION flow cell,...

Assuming you're doing this on a MinION flow cell, you can do an initial run on a Flongle flow cell to work out barcode distribution, and use that to balance the pool for MinION sequencing. We are...
Forum: Oxford Nanopore 01-31-2022, 01:39 PM
Replies: 2
Views: 4,313
Posted By gringer
All the platforms you mentioned use cluster...

All the platforms you mentioned use cluster consensus to improve single-read accuracy. This can also be done on nanopore by using more reads.

Also, the long read lengths can compensate for an...
Forum: Oxford Nanopore 01-18-2022, 06:32 PM
Replies: 1
Views: 4,104
Posted By gringer
Try needle-shearing your DNA prior to doing the...

Try needle-shearing your DNA prior to doing the CRISPR-Cas9 digest, e.g. 20 passes with a 26G or 29G needle (see here (http://www.longreadclub.org/mountain-protocol/) for more information). This has...
Forum: Oxford Nanopore 01-18-2022, 06:23 PM
Replies: 2
Views: 1,874
Posted By gringer
Also, the cDNA kits are a stranded sequencing...

Also, the cDNA kits are a stranded sequencing process (different adapter sequences for forward and reverse); you'd lose that benefit by using either the ligation kit or rapid kit on pre-prepared cDNA.
Forum: Bioinformatics 01-21-2020, 04:33 PM
Replies: 1
Views: 1,434
Posted By gringer
No. Those p-values usually apply to the...

No. Those p-values usually apply to the confidence in the value of the distinguishing statistic (a statistic which, as it happens, is frequently absent from abstracts and the non-supplementary paper...
Forum: Bioinformatics 01-21-2020, 04:25 PM
Replies: 2
Views: 8,392
Posted By gringer
Have a look at the bcftools...

Have a look at the bcftools (https://samtools.github.io/bcftools/bcftools.html) package. It supports uncompressed and gzip-compressed VCF file formats as input, as well as the BCF format, and...
Forum: Ion Torrent 08-11-2019, 01:01 AM
Replies: 19
Views: 14,572
Posted By gringer
Hobby Money

Customers don't pay return shipping to the UK. That cost is met by ONT, even for flow cells that are being returned from New Zealand. I suppose if you want to be cynical, you could say the return...
Forum: Bioinformatics 08-08-2019, 03:58 PM
Replies: 10
Views: 2,701
Posted By gringer
Maybe they used transposase tagmentation, rather...

Maybe they used transposase tagmentation, rather than directly ligating adapters onto the input DNA.
Forum: Ion Torrent 08-08-2019, 03:50 PM
Replies: 19
Views: 14,572
Posted By gringer
The MinION flow cell return to ONT is so that...

The MinION flow cell return to ONT is so that they can recycle them for use in training and internal research. If you contaminate the flow cells such that they are not safe for posting back, you...
Forum: Oxford Nanopore 05-10-2019, 01:57 AM
Replies: 6
Views: 13,551
Posted By gringer
External access

On the other side of things, a MinION sequencing run won't work unless the computer has access to the outside via non-standard ports, which are used to fetch firmware, and send telemetry data a short...
Forum: Illumina/Solexa 04-07-2019, 03:34 PM
Replies: 3
Views: 1,382
Posted By gringer
I'd expect that they do suffer from index...

I'd expect that they do suffer from index hopping, because there's a chemistry component to that as well as a machine component.
Forum: Oxford Nanopore 04-07-2019, 03:26 PM
Replies: 2
Views: 8,395
Posted By gringer
Is it possible to do a single cycle of PCR, i.e....

Is it possible to do a single cycle of PCR, i.e. the DNA equivalent of a reverse-transcription step?

I'm not sure whether you'd be able to get away with using random octamer primers - it would...
Forum: Oxford Nanopore 04-07-2019, 03:18 PM
Replies: 2
Views: 6,922
Posted By gringer
Just buy new flow cells. Anything from 2017 is...

Just buy new flow cells. Anything from 2017 is likely to be dead, and you'll get more sequence in your first hour with new flow cells than you would have got in 48 hours from working flow cells in...
Forum: Oxford Nanopore 04-07-2019, 03:12 PM
Replies: 1
Views: 8,373
Posted By gringer
Nanopore sequencing kits can be broken down into...

Nanopore sequencing kits can be broken down into two basic categories:

1. Ligation chemistry
2. Rapid adapter chemistry

The ligation chemistry produces high yields and doesn't require any...
Forum: Oxford Nanopore 04-07-2019, 03:07 PM
Replies: 1
Views: 6,855
Posted By gringer
As far as I'm aware, it doesn't matter....

As far as I'm aware, it doesn't matter. Nanopolish uses the called fastq files together with the signal in the fast5 files, so both should work. I expect the main difference between the two fast5...
Forum: Oxford Nanopore 04-07-2019, 02:55 PM
Replies: 6
Views: 13,551
Posted By gringer
Yes, as far as I'm aware all MinKNOW clients run...

Yes, as far as I'm aware all MinKNOW clients run inside their own web server, which can be connected to remotely. This is explicit with the MinIT, where the remote server is the standard way to...
Forum: Oxford Nanopore 04-07-2019, 02:48 PM
Replies: 2
Views: 7,604
Posted By gringer
Qubit or Quantus (or other similar...

Qubit or Quantus (or other similar fluorescence-based methods) are pretty much essential for nanopore sequencing. The nanodrop has issues with RNA contamination, and gives concentrations that can be...
Forum: Oxford Nanopore 04-07-2019, 02:43 PM
Replies: 2
Views: 6,813
Posted By gringer
The Starter Pack is not sufficient for doing...

The Starter Pack is not sufficient for doing multiple samples. In ONT's infinite wisdom, they decided to put the rapid kit as an option, rather than the rapid barcoding kit (despite them having...
Forum: General 02-11-2019, 09:59 PM
Replies: 1
Views: 3,589
Posted By gringer
Buy a power usage monitor (e.g. Kill-a-Watt), and...

Buy a power usage monitor (e.g. Kill-a-Watt), and stick it between things and the wall socket to measure power consumption.

Computers these days don't consume much power unless they're doing...
Forum: Oxford Nanopore 10-19-2018, 03:43 PM
Replies: 0
Views: 7,223
Posted By gringer
Flongle flow cells - now shipping

Oxford Nanopore Technologies have started shipping Flongle adapters and flow cells to customers. These are disposable flow cells using fewer pores and a cheaper design ($5000 USD for 48 flow cells)....
Forum: Oxford Nanopore 09-28-2018, 03:42 AM
Replies: 18
Views: 15,190
Posted By gringer
You need a solid-state disk as the main disk for...

You need a solid-state disk as the main disk for the computer (I'm not quite sure what "HHD" means). Other things should be fine.
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