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Forum: 454 Pyrosequencing 07-20-2012, 04:52 AM
Replies: 9
Views: 2,959
Posted By rglover
tbh that's one of the main reasons we use 454. A...

tbh that's one of the main reasons we use 454. A lot of the amplicon studies we do are protein-coding amplicons (although they're quite long compared to the OP's) and so it's easier to spot and...
Forum: 454 Pyrosequencing 07-20-2012, 03:32 AM
Replies: 9
Views: 2,959
Posted By rglover
ah, a double posting - this post is out in...

ah, a double posting - this post is out in another area of the forum too. I'd be inclined to use 454, despite the cost, because of the error rate in illumina increasing the number of 'species'...
Forum: Illumina/Solexa 07-20-2012, 03:30 AM
Replies: 4
Views: 2,093
Posted By rglover
The 454 error rate is much less than illumina -...

The 454 error rate is much less than illumina - I'm assuming you'll want to assess the number of species etc.? There have been a few papers I think saying that illumina will over-estimate the number...
Forum: Sample Prep / Library Generation 03-20-2012, 06:09 AM
Replies: 10
Views: 6,498
Posted By rglover
We do this kind of work (sequencing ssRNA plant...

We do this kind of work (sequencing ssRNA plant virus genomes) routinely using 454. We multiplex to make it more cost effective and have had entire viral genomes with very few sequences (<10,000...
Forum: Academic/Non-Profit Jobs 03-12-2012, 01:28 AM
Replies: 0
Views: 1,370
Posted By rglover
Post doc: Jointly between York uni and FERA (NGS bioinformatics)

A bioinformatics postdoc position is available jointly between the University of York and the UK Food and Environment Research Agency, also in York.

Job description can be found here:...
Forum: 454 Pyrosequencing 01-16-2012, 06:29 AM
Replies: 3
Views: 7,930
Posted By rglover
454 FLX+ with amplicons - anyone tried it?

I guess the title says it all - has anyone tried sequencing amplicons on an FLX+ yet? We're looking at trying it in the next month or two and I was wondering whether anyone else had tried it already...
Forum: Bioinformatics 10-13-2011, 06:41 AM
Replies: 9
Views: 3,484
Posted By rglover
What's the problem with using the tools that are...

What's the problem with using the tools that are already available?
Forum: Site Feedback/Suggestions 10-10-2011, 06:12 AM
Replies: 430
Views: 82,875
Posted By rglover
I like that opening a lot and "SeqAnswers was...

I like that opening a lot and "SeqAnswers was founded" seems a much nicer fit.

Just done a quick edit of the SeqAnswers in google searches part to make it a little more succinct - word count now...
Forum: Site Feedback/Suggestions 10-10-2011, 04:20 AM
Replies: 430
Views: 82,875
Posted By rglover
You could drop the "We reckon" at the start of...

You could drop the "We reckon" at the start of paragraph 3. It's quite a casual couple of words and dropping it would make the "SEQanswers is uniquely positioned in the HTS field" more definitive and...
Forum: Bioinformatics 09-15-2011, 08:18 AM
Replies: 6
Views: 9,961
Posted By rglover
report writing distraction technique :) I'm not...

report writing distraction technique :) I'm not normally someone who answers "my code doesn't work" questions...
Forum: Bioinformatics 09-15-2011, 07:29 AM
Replies: 6
Views: 9,961
Posted By rglover
Hi Semna, There are a number of things that...

Hi Semna,

There are a number of things that are making your code not work, but first a few pointers:

Enclosing your code in code tagsis a really good idea if you want people to help you out -...
Forum: 454 Pyrosequencing 09-05-2011, 05:29 AM
Replies: 6
Views: 3,151
Posted By rglover
454 website hiccup?

The 454 website (including my454) seems to be down and ads are up in its place. http://www.454.com/my454/index.asp

It looks suspiciously like Roche have forgotten to renew the domain...
Forum: Bioinformatics 09-02-2011, 08:10 AM
Replies: 10
Views: 20,259
Posted By rglover
yes, that's possible - you'll need to create a...

yes, that's possible - you'll need to create a blast database from the sequences you want to search against:

makeblastdb -in sequences.fasta -dbtype nucl

Then you'd blast as normal, but the...
Forum: 454 Pyrosequencing 08-30-2011, 05:14 AM
Replies: 23
Views: 6,491
Posted By rglover
Personally, as I stated above, I would rather pay...

Personally, as I stated above, I would rather pay for the maintenance wash kits than have Roche refuse to fix a problem with our machine because we hadn't bought them. We had to fight for the money...
Forum: 454 Pyrosequencing 08-26-2011, 07:27 AM
Replies: 23
Views: 6,491
Posted By rglover
We've been under the impression that if we have a...

We've been under the impression that if we have a problem with our 454 and Roche don't see that we've been buying maintenance kits they could refuse to fix the problem because we can't say we've been...
Forum: De novo discovery 03-11-2011, 04:34 AM
Replies: 10
Views: 4,166
Posted By rglover
The website seems to be back up...

The website seems to be back up (http://cs.stanford.edu/genovo) - I'm just trying it out on a small metagenomic dataset (65000 seqs) to see how it compares on our data.
I've not tried velvet on our...
Forum: De novo discovery 03-10-2011, 05:36 AM
Replies: 10
Views: 4,166
Posted By rglover
I've just read the paper, although the link for...

I've just read the paper, although the link for downloading the software keeps giving a 404 error... I'd love to give it a go on my metagenome datasets though to see how it compares to CLCbio too...
Forum: Bioinformatics 03-07-2011, 02:17 AM
Replies: 2
Views: 5,771
Posted By rglover
What version of the NCBI executables are you...

What version of the NCBI executables are you using? What command line arguments are you using to create your database?
Forum: Service Providers 02-22-2011, 06:20 AM
Replies: 14
Views: 13,358
Posted By rglover
Hi, We do contract bioinformatics here at Fera...

Hi,
We do contract bioinformatics here at Fera (in York). If you fancy a chat send me a PM - I could give you a call to discuss if you'd like.
Cheers,
Rachel
Forum: Bioinformatics 02-16-2011, 09:06 AM
Replies: 4
Views: 10,539
Posted By rglover
try setting the environment variable BLASTDB to...

try setting the environment variable BLASTDB to the location of your database, that should do the trick.
Forum: Core Facilities 12-14-2010, 08:18 AM
Replies: 16
Views: 9,588
Posted By rglover
...there's always absolute ethanol for those...

...there's always absolute ethanol for those desperate enough :eek: :p
Forum: Introductions 09-24-2010, 01:48 AM
Replies: 1
Views: 1,090
Posted By rglover
Hi Anthony, Hello from someone "oop norf" (I'm...

Hi Anthony,
Hello from someone "oop norf" (I'm at FERA, http://www.defra.gov.uk/fera). I've a feeling we'll probably cross paths at some point as we're doing bacterial sequencing too (as well as...
Forum: Bioinformatics 08-20-2010, 08:42 AM
Replies: 8
Views: 13,438
Posted By rglover
I'm at the same institute as Ben - rather than...

I'm at the same institute as Ben - rather than use BioPerl (the Blast writer section has always been a bit of a pain to get working correctly) we hashed together a script that would do what he wanted...
Forum: Events / Conferences 08-19-2010, 04:30 AM
Replies: 1
Views: 3,106
Posted By rglover
I've just graduated from the distance learning...

I've just graduated from the distance learning MSc (when it was called MSc Bioinformatics) and can definitely recommend it :)
Forum: Bioinformatics 08-09-2010, 01:13 AM
Replies: 8
Views: 3,433
Posted By rglover
No problem - I'm sure I've seen most Blast+...

No problem - I'm sure I've seen most Blast+ errors in the last couple of years. The manual isn't exactly the most user-friendly of documents :) You really have to dig around for the information you...
Showing results 1 to 25 of 51

 


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