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Forum: General 03-28-2017, 11:10 AM
Replies: 2
Views: 1,320
Posted By Anthony.287
Thank you! I'll check that out.

Thank you! I'll check that out.
Forum: General 03-27-2017, 11:43 AM
Replies: 2
Views: 1,320
Posted By Anthony.287
SPR resources?

Hello,
I know this isn’t sequencing related, but I was wondering if anybody knew of any online groups such as this one that is catered to Surface Plasmon Resonance machines? Specifically, the GE...
Forum: Sanger/Dye Terminator 06-01-2016, 06:28 AM
Replies: 7
Views: 6,802
Posted By Anthony.287
Thanks for all of the info and suggestions! I...

Thanks for all of the info and suggestions! I agree, these things are waaay overpriced. I ended up ordering a refurbished one from LabX. We've been having some other issues with our sequencing and I...
Forum: Sanger/Dye Terminator 05-31-2016, 11:03 AM
Replies: 7
Views: 6,802
Posted By Anthony.287
Heat Sealer Needed!

Hello everybody!
Our 96-well plate heat sealer died in a fit of smoke and flame this morning. Replacement sealers are in the thousands of dollars!! All we want is something like this...
Forum: 454 Pyrosequencing 10-30-2014, 09:02 AM
Replies: 3
Views: 1,589
Posted By Anthony.287
That depends on the primers used to create the...

That depends on the primers used to create the amplicons. :) You can use Lib-L primer sequences to create amplicons, which is what all of my previous 16s customers were doing. You end up with...
Forum: 454 Pyrosequencing 10-28-2014, 04:50 AM
Replies: 11
Views: 7,815
Posted By Anthony.287
Hello! I can't speak much about the Jr, but...

Hello!
I can't speak much about the Jr, but with the upgraded FLX I saw many odd results when mixing Titanium chemistry with +. For example, following the titanium emPCR instructions and sequencing...
Forum: 454 Pyrosequencing 10-17-2014, 10:05 AM
Replies: 3
Views: 1,589
Posted By Anthony.287
XL+ vs. FLX FYI

Just an FYI for anyone still using the XL+. It's a bad idea to run any FLX samples on the XL+ chemistry. From what was sort of explained to me by a 454 rep, the emPCR master mix and thermocycling...
Forum: Bioinformatics 01-10-2014, 06:54 AM
Replies: 5
Views: 1,180
Posted By Anthony.287
Revisiting Linux distributions...

Morning!
First, a bit of background. Currently, my lab (a core facility) is using the 454 FLX+. Our data rig, which we use for the Roche software suite and not much else, is running RHEL 6, and our...
Forum: 454 Pyrosequencing 10-11-2013, 08:50 AM
Replies: 0
Views: 1,618
Posted By Anthony.287
Paired-end data question

Hello all!
I have a question about paired-end data. We have a client who is trying to gain information about a 2Kb region from a 750Kb genome and is planning to get several runs worth of FLX+ data....
Forum: 454 Pyrosequencing 06-18-2013, 07:52 AM
Replies: 0
Views: 1,353
Posted By Anthony.287
Running without a PTP or gasket?

Hello all!
So, we finally got our FLX upgraded to the +, and had it done at the factory. During the installation here in the lab, the engineer performed one or more install validation scripts...
Forum: 454 Pyrosequencing 02-12-2013, 06:37 AM
Replies: 7
Views: 2,125
Posted By Anthony.287
Number6, I'll look into that. That could be...

Number6, I'll look into that. That could be helpful.

Martin2, I think you misunderstood the question. I want to be able to look at reads that don't sort to any barcode. It doesn't matter how they...
Forum: 454 Pyrosequencing 01-28-2013, 12:43 PM
Replies: 3
Views: 1,722
Posted By Anthony.287
If you mean the FLX+, then no. We're using the...

If you mean the FLX+, then no. We're using the FLX titanium, with software 2.5.3.
Forum: 454 Pyrosequencing 01-25-2013, 11:04 AM
Replies: 21
Views: 9,593
Posted By Anthony.287
1) Definitely agree. The ratios of aqueous : oil...

1) Definitely agree. The ratios of aqueous : oil do not match up across the kits, and this seems to have an effect. I've compensated by making sure to use the same lot numbers and same size kits for...
Forum: 454 Pyrosequencing 01-25-2013, 10:49 AM
Replies: 7
Views: 2,125
Posted By Anthony.287
Thank you! I'll give that a try.

Thank you! I'll give that a try.
Forum: 454 Pyrosequencing 01-24-2013, 08:38 AM
Replies: 7
Views: 2,125
Posted By Anthony.287
How to sort with sfffile/sffinfo...

Hey all!
I've got an unusual request. I want to be able to access just the reads that do not match any barcodes. I can easily sort reads into .sffs based on barcodes, but I want to look at the reads...
Forum: 454 Pyrosequencing 12-13-2012, 01:20 PM
Replies: 3
Views: 1,722
Posted By Anthony.287
Errors in barcodes

Hello, again!
I’ve been getting into the informatics side of 454 sequencing more lately, and have some questions. Mostly about barcodes…
1. Does anybody look for barcodes that shouldn’t be in a...
Forum: 454 Pyrosequencing 12-07-2012, 06:07 AM
Replies: 2
Views: 986
Posted By Anthony.287
Thank you! That's what I figured, but needed to...

Thank you!
That's what I figured, but needed to make sure.
Thanks again!
Forum: 454 Pyrosequencing 12-06-2012, 12:46 PM
Replies: 2
Views: 986
Posted By Anthony.287
FLX beads on JR?

Will capture beads for the FLX sequence on the JR? We have a FLX and are looking to sequence a library on a JR somewhere else, for quality control purposes. So, we'd create the library, do emPCR, and...
Forum: 454 Pyrosequencing 12-06-2012, 12:32 PM
Replies: 8
Views: 2,743
Posted By Anthony.287
Thank you for the link! Just starting to get the...

Thank you for the link! Just starting to get the hang of sfftools, and it looks like I'm finding the same...
Forum: 454 Pyrosequencing 12-06-2012, 12:30 PM
Replies: 1
Views: 1,446
Posted By Anthony.287
RLMIDs vs GSMIDs

Hello all!
I'm finally starting to get the hang of sfffile, and am finding some things that I can't explain. For instance, one particular region (a pool of 4 RLMID tagged rapid libraries) on the...
Forum: 454 Pyrosequencing 11-15-2012, 06:02 AM
Replies: 8
Views: 2,743
Posted By Anthony.287
JackieBadger, Any chance you could help me find...

JackieBadger,
Any chance you could help me find that paper? We're dealing with a similar issue, and trying to rule out anything and everything is rather time consuming.
Thanks!!
Forum: 454 Pyrosequencing 08-21-2012, 11:41 AM
Replies: 1
Views: 1,521
Posted By Anthony.287
Automated AMPure Purification

Hello again!
Does anyone have any experience doing the AMPureXP purification of amplicons on a robot? Specifically, we have a Biomek FX with standard CleanSEQ and AMPure protocols. These don't match...
Forum: 454 Pyrosequencing 08-21-2012, 11:34 AM
Replies: 3
Views: 1,180
Posted By Anthony.287
Thank you! This sounds like the voice of...

Thank you!
This sounds like the voice of experience...
Forum: 454 Pyrosequencing 08-21-2012, 10:00 AM
Replies: 3
Views: 1,180
Posted By Anthony.287
Frozen Supplement CB

Hello all!
I noticed yesterday that one tube of Supplement CB had frozen solid. Apparently the refrigerator that it was in got a bit too cold! Does anyone know what this reagent is, and if it is now...
Forum: 454 Pyrosequencing 07-27-2012, 03:59 PM
Replies: 1
Views: 1,379
Posted By Anthony.287
Yeah, this seems to be happening for a lot of...

Yeah, this seems to be happening for a lot of users. I've ad to go all the way to 32 cpb to get 8% with an amplicon pool. No idea why.
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