SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 500
Search took 0.03 seconds.
Search: Posts Made By: gringer
Forum: Ion Torrent 08-11-2019, 01:01 AM
Replies: 19
Views: 2,174
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: 1,174
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: 2,174
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: 5
Views: 2,922
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: 697
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: 1,729
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: 1
Views: 1,318
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: 2,230
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: 1,801
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: 5
Views: 2,922
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: 2,437
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: 1,429
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: 3
Views: 2,386
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: 2,207
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: 14
Views: 6,593
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.
Forum: Sample Prep / Library Generation 09-04-2018, 03:21 AM
Replies: 4
Views: 1,549
Posted By gringer
OpenTrons

If you want cheap, there's the OpenTrons OT-2 (http://opentrons.com/ot-2). The basic system is $3500 USD, with additional modules ordered separately:


single channel pipette $500
8-channel...
Forum: Bioinformatics 09-04-2018, 02:43 AM
Replies: 2
Views: 848
Posted By gringer
Use supertranscripts as your reference genome: ...

Use supertranscripts as your reference genome:

https://github.com/Oshlack/Lace/wiki

https://github.com/trinityrnaseq/trinityrnaseq/wiki/SuperTranscripts
Forum: Bioinformatics 08-05-2018, 05:53 AM
Replies: 1
Views: 986
Posted By gringer
What is the question you are trying to answer by...

What is the question you are trying to answer by doing this mapping?
Forum: Bioinformatics 08-05-2018, 05:32 AM
Replies: 104
Views: 31,772
Posted By gringer
Wow! Joined in 2014, only one post, and you chose...

Wow! Joined in 2014, only one post, and you chose to make your first post something about mutant clouds in response to a 3-year old post of mine from the first page of this thread. I'm not sure if I...
Forum: Oxford Nanopore 05-30-2018, 05:29 AM
Replies: 1
Views: 2,667
Posted By gringer
Clive Brown's Technology Talk from London Calling 2018

For the last 4 years I've attended Oxford Nanopore Technologies' yearly London Calling conference. One of the interesting bits of this conference is the talk from Clive Brown about what's happening...
Forum: Bioinformatics 05-28-2018, 05:20 AM
Replies: 1
Views: 722
Posted By gringer
That should be fine. Inchworm does a kmer-based...

That should be fine. Inchworm does a kmer-based assembly, so as long as the reads are longer than the size of the kmers, it should be okay.

However, it'd be a good idea to do adapter and end...
Forum: Bioinformatics 04-22-2018, 04:31 AM
Replies: 2
Views: 602
Posted By gringer
If you don't care about accuracy, just...

If you don't care about accuracy, just concatenate all the fasta sequences into a single large sequence....

More seriously, you're probably not going to get any better continuity from your data...
Forum: Bioinformatics 04-22-2018, 04:25 AM
Replies: 13
Views: 2,043
Posted By gringer
That's not the only reason. Sigma also has...

That's not the only reason. Sigma also has region-specific pricing. Without logging in, I choose the location when I first visit the site (presumably stored as a cookie for subsequent visits), and...
Forum: Bioinformatics 04-22-2018, 03:00 AM
Replies: 13
Views: 2,043
Posted By gringer
You won't be able to get a good de-novo assembly...

You won't be able to get a good de-novo assembly from Illumina data alone, and longer SBS reads won't fix that. Consider things like 28S rRNA gene regions, where kilobase-length regions are repeated...
Forum: Bioinformatics 04-20-2018, 04:25 PM
Replies: 13
Views: 2,043
Posted By gringer
As far as I know, ONT is the only sequencing...

As far as I know, ONT is the only sequencing machine supplier that publishes all their prices on their store website; you can have a look and see for yourself!

At the moment marginal cost per base...
Showing results 1 to 25 of 500

 


All times are GMT -8. The time now is 04:35 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO