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Forum: Oxford Nanopore 12-15-2021, 06:49 AM
Replies: 2
Views: 3,585
Posted By jhalpin
ONT sequencing kits

In our lab, we had trouble getting long DNA from the extractions and so the rapid kit didn't work for us. It has a built in fragmentation step that also applies the adapters/barcodes. The ligation...
Forum: Oxford Nanopore 09-09-2020, 07:23 AM
Replies: 18
Views: 15,203
Posted By jhalpin
Hi everyone! We've been dabbling with nanopore...

Hi everyone! We've been dabbling with nanopore off and on for a little over a year. Recently, I've been trying the Ligation sequencing kit with native barcoding on a version 9 flowcell. The DNA...
Forum: Sample Prep / Library Generation 04-15-2019, 07:04 AM
Replies: 6
Views: 2,452
Posted By jhalpin
How did you measure your 100ng input?

How did you measure your 100ng input?
Forum: Bioinformatics 04-01-2019, 10:41 AM
Replies: 7
Views: 1,776
Posted By jhalpin
Sorry.. in the lab to make sequencing libraries...

Sorry.. in the lab to make sequencing libraries the primers are added. They aren't in the sequence of the thing you're looking at. The primers are constructed by a company and sold as part of the...
Forum: Bioinformatics 04-01-2019, 09:49 AM
Replies: 7
Views: 1,776
Posted By jhalpin
Primers and adapters are added to the fragments...

Primers and adapters are added to the fragments during the preparation of the samples. They are not native sequences and are extremely over represented compared to any natural occurrences of those...
Forum: General 04-01-2019, 06:42 AM
Replies: 4
Views: 3,438
Posted By jhalpin
If there is a mistake in your adapter ligation...

If there is a mistake in your adapter ligation you may not get amplification, since the indices are the primers for amplification. It would also account for the large number of dimers, potentially.
Forum: Ion Torrent 03-19-2019, 05:53 AM
Replies: 3
Views: 7,250
Posted By jhalpin
S5 chips drying out

Hello,

We have not seen this problem.. are the chips very old? Or stored at high temperatures? If they are not old and have been stored appropriately, I'd contact Ion Torrent and see if they'll...
Forum: Ion Torrent 06-15-2018, 09:27 AM
Replies: 4
Views: 7,443
Posted By jhalpin
Opentrons Automated Pipetting System

Has anyone here used the Opentrons OT-2 for library preparation? https://opentrons.com/ot-2 (http://opentrons.com/ot-2)
Forum: Ion Torrent 05-02-2018, 09:06 AM
Replies: 2
Views: 4,513
Posted By jhalpin
What method are you using to load it? What...

What method are you using to load it? What library prep kit are you using?
Forum: Ion Torrent 05-02-2018, 07:07 AM
Replies: 9
Views: 10,333
Posted By jhalpin
We have an S5 that we're using 400bp chemistry...

We have an S5 that we're using 400bp chemistry on. It's been doing pretty well and is SO much easier to use than the PGM.

Can anyone comment on the 600bp kit? How is the size selection with it?
Forum: Oxford Nanopore 01-30-2018, 11:07 AM
Replies: 4
Views: 14,016
Posted By jhalpin
Thanks for the clarification.. I was having a...

Thanks for the clarification.. I was having a hard time with Oxford's information on run vs sample.
Forum: Oxford Nanopore 01-30-2018, 06:34 AM
Replies: 4
Views: 14,016
Posted By jhalpin
I am also curious about costs. I'd like to run...

I am also curious about costs. I'd like to run multiplex bacterial genomes and it looks like from the oxford site I can use either the 1d or 1d2 kit. Is it reasonable to run 12 4Mb genomes on one...
Forum: Bioinformatics 04-19-2017, 05:46 AM
Replies: 7
Views: 2,456
Posted By jhalpin
... you have single end Illumina data? Is that a...

... you have single end Illumina data? Is that a thing?

We use Ion Torrent technology, but if I see that it's usually a size selection problem.. something went wrong with my bead ratios.
Forum: General 03-30-2017, 11:08 AM
Replies: 0
Views: 1,365
Posted By jhalpin
Question streptavidin losing magnetic properties?

Anyone have any experience with streptavidin beads losing their magnetic properties? They have not been boiled nor frozen. It's for an antibody binding assay and it's really random as to which...
Forum: Ion Torrent 02-01-2017, 10:41 AM
Replies: 15
Views: 7,903
Posted By jhalpin
I don't know the solution, but I can tell you Ion...

I don't know the solution, but I can tell you Ion Torrent has a lot of deletion errors that are sequencing artifacts when sequencing through a long (>5bp) homopolymer region. If this is where your...
Forum: Ion Torrent 05-20-2016, 09:42 AM
Replies: 8
Views: 8,408
Posted By jhalpin
Out of curiosity, does the NEB kit have less...

Out of curiosity, does the NEB kit have less cleanup steps?
Forum: Ion Torrent 02-18-2016, 06:37 AM
Replies: 8
Views: 8,408
Posted By jhalpin
Talking I have not used the NEBnext kit, but I do...

I have not used the NEBnext kit, but I do regularly use the Kapa BioSciences kit for IonTorrent libraries. It is significantly less expensive than the Life Tech kit and I get much much better...
Forum: Ion Torrent 04-10-2015, 01:55 PM
Replies: 0
Views: 1,649
Posted By jhalpin
Question Double sided SPRI for size selection -- Ion Library

Has anyone tried double-sided SPRI size selection in place of the e-gel? How did it work?
Forum: Ion Torrent 03-06-2015, 07:28 AM
Replies: 2
Views: 2,231
Posted By jhalpin
In case anyone is wondering, it wasn't the tween....

In case anyone is wondering, it wasn't the tween. I tried to run this pool again yesterday and got the same results. Measured the pool by qubit (should have been ~30ng/mL) and it was too low to...
Forum: Ion Torrent 03-06-2015, 07:18 AM
Replies: 3
Views: 3,059
Posted By jhalpin
Allright, fixing the Tris concentration didn't...

Allright, fixing the Tris concentration didn't fix my problem. I'm inputting 200 ng and getting 0.02 ng/ul at the end of library prep. It's technically enough to sequence but it's really low.. I'd...
Forum: Sample Prep / Library Generation 03-05-2015, 11:46 AM
Replies: 0
Views: 1,200
Posted By jhalpin
Question MiSeq -- Kapa Library Kit for Clostridia?

Has anyone tried one of Kapa's library kits on Clostrida ssp or another AT rich organism? It's supposed to show less bias due to GC content. What was your result?
Forum: Sample Prep / Library Generation 03-05-2015, 11:39 AM
Replies: 0
Views: 1,659
Posted By jhalpin
Question Ion Torrent -- KAPA library kit -- Any impressions?

Has anyone tried Kapa's kit for Ion Torrent libraries? How'd it work?

http://www.kapabiosystems.com/product-applications/platforms/ion-torrent/library-preparation-for-ion-torrent/
Forum: Ion Torrent 02-02-2015, 09:29 AM
Replies: 3
Views: 3,059
Posted By jhalpin
Red face Well huh. Looking back at my notes I wrote down...

Well huh. Looking back at my notes I wrote down 10 mM. Not sure when/how that turned into 100 mM. I guess I know why my libraries are weird now.

I'll check out the Q columns, too. Thanks!
Forum: Ion Torrent 01-30-2015, 01:39 PM
Replies: 2
Views: 2,231
Posted By jhalpin
Angry So I had a sudden flashback to mixing the melt...

So I had a sudden flashback to mixing the melt off solution and thinking it didn't look "sudsy". It's entirely possible I put water in instead of tween, since the bottles are exactly the same. Has...
Forum: Ion Torrent 01-30-2015, 01:11 PM
Replies: 2
Views: 2,231
Posted By jhalpin
Question PGM: No loading on 316v2 chip

Hello,

I ran a 316v2 chip today for the 2nd run of an initialization. My chip has 2% loading.. could this be a templating or enrichment failure? My QC percentage was 7.24%. Low, but we've had...
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