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Forum: Sample Prep / Library Generation 11-22-2016, 04:52 PM
Replies: 3
Views: 1,962
Posted By ScottC
Anyone optimised ATAC-seq for Nextera XT?

Hi there,

Has anyone tried/optimised ATAC-seq using Nextera XT?

Cheers,

Scott.
Forum: Sample Prep / Library Generation 11-22-2016, 04:30 PM
Replies: 69
Views: 42,165
Posted By ScottC
Does anyone here use NexteraXT rather than...

Does anyone here use NexteraXT rather than Nextera for ATAC-seq library construction?
Forum: Oxford Nanopore 10-12-2016, 09:25 PM
Replies: 1
Views: 1,441
Posted By ScottC
Technically, the kit allows 6 washes.

Technically, the kit allows 6 washes.
Forum: Illumina/Solexa 09-22-2016, 04:00 PM
Replies: 28
Views: 3,193
Posted By ScottC
A couple of things: - BaseSpace will still...

A couple of things:

- BaseSpace will still do basecalling for free from instrument runs.
- The newest version of bcl2fastq2 will now treat N bases properly (as 'wildcards' so-to-speak)

Also,...
Forum: General 04-14-2016, 03:22 PM
Replies: 5
Views: 1,339
Posted By ScottC
Yes. What in particular did you want to know?

Yes. What in particular did you want to know?
Forum: Illumina/Solexa 04-05-2016, 04:04 PM
Replies: 1
Views: 764
Posted By ScottC
In our experience, the NextSeq is by far the most...

In our experience, the NextSeq is by far the most tolerant of the Illumina systems in terms of pushing the cluster numbers (second after that is the old GA/II/IIx), although the patterned flowcells...
Forum: Illumina/Solexa 02-16-2016, 08:25 PM
Replies: 4
Views: 809
Posted By ScottC
Hi, If I were looking for this kit, I'd...

Hi,

If I were looking for this kit, I'd double-check that the Illumina representative knows that you are after the 'old' mate-pair kit... Last year, we were told that it had been discontinued....
Forum: Illumina/Solexa 11-18-2015, 04:32 PM
Replies: 5
Views: 2,132
Posted By ScottC
We have seen quite poor performance on the...

We have seen quite poor performance on the NextSeq with low diversity libraries. We used up to 50% PhiX with little/no improvement... that being said, the low diversity libraries that we have tried...
Forum: Illumina/Solexa 09-20-2015, 03:09 PM
Replies: 4
Views: 1,049
Posted By ScottC
Until this year, we have had the PM carried out,...

Until this year, we have had the PM carried out, but have decided against it this year.

If it helps you decided, you can ask your Illumina FSE to give you a list of the things they will do to the...
Forum: Illumina/Solexa 08-09-2015, 02:31 PM
Replies: 12
Views: 3,292
Posted By ScottC
Hi. This is fairly obvious, but did you try...

Hi. This is fairly obvious, but did you try changing the configuration files like you would do with the MiSeq? They're not exactly the same, of course, but there's an field <SaveCifs> in...
Forum: Illumina/Solexa 07-21-2015, 09:27 PM
Replies: 10
Views: 5,517
Posted By ScottC
Hi. We save the intensity files from our...

Hi.

We save the intensity files from our MiSeq for certain run types. We have both of the configuration files on our instrument. Be aware that one file (MiSeq.Configuration.xml) is on the C...
Forum: Illumina/Solexa 06-10-2015, 03:03 PM
Replies: 68
Views: 18,742
Posted By ScottC
I have had the same experience... The...

I have had the same experience...

The quality seems to drop quite badly. For us, it's often about half way through the read. But, our libraries on 2x300b runs are almost always low diversity so I...
Forum: Illumina/Solexa 03-05-2015, 07:04 PM
Replies: 3
Views: 1,396
Posted By ScottC
As an aside... I found it interesting that the V2...

As an aside... I found it interesting that the V2 and V3 miseq reagents are different colours.
Forum: Illumina/Solexa 02-19-2015, 01:26 PM
Replies: 3
Views: 1,498
Posted By ScottC
Hi, I don't think you'll be able to do...

Hi,

I don't think you'll be able to do another run with 0 bases, because the instrument will try to carry out clustering again, which would probably be bad for your already clustered flowcell.
...
Forum: Illumina/Solexa 02-18-2015, 01:51 PM
Replies: 8
Views: 2,529
Posted By ScottC
You can also ask them for some library...

You can also ask them for some library statistics... concentration of the final library and fragment size range (usually Bioanalyzer/Tapestation results). Sometimes you will see good first-read...
Forum: Sample Prep / Library Generation 02-05-2015, 03:58 PM
Replies: 1
Views: 1,258
Posted By ScottC
... or, has anyone out there used regular Taq to...

... or, has anyone out there used regular Taq to produce libraries? I guess that would answer the question about whether it will work. I think I recall someone in a thread about 16S survey sequencing...
Forum: Illumina/Solexa 12-18-2014, 04:45 PM
Replies: 9
Views: 3,238
Posted By ScottC
Yes, people use it for a variety of different...

Yes, people use it for a variety of different purposes, but it's actual intended purpose is simply as a catch-all for any read that wasn't assignable to a sample for any reason (poor quality,...
Forum: Illumina/Solexa 12-02-2014, 03:46 PM
Replies: 2
Views: 1,565
Posted By ScottC
Hi Esherman, All the flowcells are the same,...

Hi Esherman,

All the flowcells are the same, at least for "standard yield" kits. You can use them regardless of the kit version they came with (I know this from experience). The chemistry is...
Forum: Illumina/Solexa 11-13-2014, 01:48 PM
Replies: 18
Views: 5,579
Posted By ScottC
Try this: ...

Try this:

http://supportres.illumina.com/documents/documentation/chemistry_documentation/16s/16s-metagenomic-library-prep-guide-15044223-b.pdf

Also, I'm not sure you need the extra N bases to...
Forum: Illumina/Solexa 11-09-2014, 01:38 PM
Replies: 6
Views: 2,402
Posted By ScottC
Some things that we've experienced with slow...

Some things that we've experienced with slow migration: Does the priming syringe return to the recommended level after you release the clamp? Are all your reagents within their expiry date? Is the...
Forum: Events / Conferences 10-14-2014, 05:39 PM
Replies: 0
Views: 1,249
Posted By ScottC
Do you need to learn or refresh your molecular biology theory and lab bench skills?

The Micromon Recombinant DNA Techniques Course is running again this year, as it has for over 25 years. Have you been out of the lab for a while? Have a scientific background, but not that familiar...
Forum: Illumina/Solexa 08-20-2014, 06:18 PM
Replies: 5
Views: 2,604
Posted By ScottC
Ask them if any parts have been replaced - they...

Ask them if any parts have been replaced - they sometimes need a new valve block (there are at least 2 different versions of the valve block). We've had valve blocks and servo motors replaced on...
Forum: Core Facilities 08-10-2014, 03:36 PM
Replies: 1
Views: 1,573
Posted By ScottC
What are you trying to get it to do, that you...

What are you trying to get it to do, that you can't do with the software that was designed to control the robot?
Forum: Illumina/Solexa 08-08-2014, 04:51 PM
Replies: 7
Views: 3,291
Posted By ScottC
Hi, A good place to start is the Illumina...

Hi,

A good place to start is the Illumina adapter sequence letter:
...
Forum: Illumina/Solexa 08-07-2014, 07:12 PM
Replies: 3
Views: 1,653
Posted By ScottC
No, I mean that the software doesn't necessarily...

No, I mean that the software doesn't necessarily look at a circular cluster. It can take a section through the middle of a cluster, avoiding the edges, to 'rescue' overlapping clusters that may have...
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