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Forum: Illumina/Solexa 10-08-2018, 12:47 PM
Replies: 3
Views: 808
Posted By JoeKutch
Have you tried talking to the staff at your core...

Have you tried talking to the staff at your core to find out why the turnaround is so long? I doubt their MiSeq is being used to capacity, so there must be a specific spot where it's being held up. ...
Forum: Sample Prep / Library Generation 08-10-2018, 09:31 AM
Replies: 2
Views: 875
Posted By JoeKutch
Thanks for the reply Philip: I don't think...

Thanks for the reply Philip:

I don't think they are overloaded, but I can dilute further and try them again with some other samples. Qubit and then diluting should have prevented that.

They...
Forum: Sample Prep / Library Generation 08-08-2018, 01:09 PM
Replies: 2
Views: 875
Posted By JoeKutch
Bioanalyzing long ATAC-Seq libraries

Hi All,

I am part of a sequencing core, trying to QC a client's ATAC-Seq libraries via the bioanalyzer on a DNA high sensitivity chip. Prior to running the samples I checked the concentrations...
Forum: General 04-23-2018, 11:01 AM
Replies: 4
Views: 4,176
Posted By JoeKutch
http://enseqlopedia.com/ngs-mapped/ This map...

http://enseqlopedia.com/ngs-mapped/

This map on James Hadfield's blog about NGS has a good map, I believe he updated it back in January.
Forum: Illumina/Solexa 03-12-2018, 07:41 AM
Replies: 3
Views: 1,285
Posted By JoeKutch
As far as I understand, the MiSeq, HiSeq 2500,...

As far as I understand, the MiSeq, HiSeq 2500, and HiSeq 4000 each have a single camera. The flow cell is divided into lanes, swaths (left/right/center depending on the machine), surfaces (top and...
Forum: Illumina/Solexa 02-02-2018, 12:41 PM
Replies: 6
Views: 1,279
Posted By JoeKutch
From your post I can't be sure, but it sounds...

From your post I can't be sure, but it sounds like you're sequencing your Nextera libraries on a NextSeq. If your loading concentration is resulting in 140K/mm2 densities, you can start by targeting...
Forum: Illumina/Solexa 01-18-2018, 02:41 PM
Replies: 6
Views: 849
Posted By JoeKutch
That's true, yes. But are lanes 1/3 and 2/4...

That's true, yes. But are lanes 1/3 and 2/4 treated as a single continuous lane with SBS flowing through 1 and then into 3, or does the line split and feed both of them? I always thought it was the...
Forum: Illumina/Solexa 01-18-2018, 10:55 AM
Replies: 6
Views: 849
Posted By JoeKutch
Without knowing the cluster densities reported by...

Without knowing the cluster densities reported by your instrument, I couldn't say.

What are the average densities for each of the 4 lanes, and the number of raw and PF reads for each lane?

Our...
Forum: Illumina/Solexa 01-18-2018, 10:29 AM
Replies: 6
Views: 849
Posted By JoeKutch
Intensity =/= cluster density, though they are...

Intensity =/= cluster density, though they are related. There can be variations in intensity from imperfections in the flow cell, smudges on the surface, and focusing. Even reagent age/batch.

The...
Forum: Illumina/Solexa 07-19-2017, 08:21 PM
Replies: 7
Views: 1,420
Posted By JoeKutch
Sorry - it looks like I misunderstood, not you. ...

Sorry - it looks like I misunderstood, not you.

I think the added sequencing primer bases are meant to keep the Tm of the primer in the appropriate range for the sequencer. For example, when...
Forum: Illumina/Solexa 07-19-2017, 01:55 PM
Replies: 7
Views: 1,420
Posted By JoeKutch
I think what he's trying to say is that those are...

I think what he's trying to say is that those are the sequences needed to actually bind the template to the oligonucleotide lawn on the flow cell.
Forum: Illumina/Solexa 07-19-2017, 10:23 AM
Replies: 22
Views: 4,146
Posted By JoeKutch
Looking at your run metrics, I think your...

Looking at your run metrics, I think your phasing/prephasing seems high, which could indicate a clog/leak in your machine's fluidics. Our MiSeq had a similar problem a while back where we were only...
Forum: Illumina/Solexa 05-09-2017, 08:11 AM
Replies: 14
Views: 8,851
Posted By JoeKutch
This Illumina support bulletin lists the...

This Illumina support bulletin lists the positions, total volumes, and final concentrations of the sequencing and index primers for all the sequencers that support custom primers.
...
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