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Forum: Illumina/Solexa 02-09-2018, 08:47 AM
Replies: 3
Views: 482
Posted By GW_OK
Well, yeah, but that's some serious capex burn.

Well, yeah, but that's some serious capex burn.
Forum: Sample Prep / Library Generation 02-09-2018, 07:43 AM
Replies: 2
Views: 505
Posted By GW_OK
Is there a reason you can't draw into a PAXgene...

Is there a reason you can't draw into a PAXgene tube?
Forum: Illumina/Solexa 02-09-2018, 07:17 AM
Replies: 3
Views: 482
Posted By GW_OK
Wow. I wonder who surplused $5M in...

Wow. I wonder who surplused $5M in instrumentation?
Forum: Illumina/Solexa 02-09-2018, 06:42 AM
Replies: 6
Views: 495
Posted By GW_OK
Custom primers have nothing to do with generation...

Custom primers have nothing to do with generation of clusters. Both ends of the library adapters must have the requisite P5 and P7 sites for proper bridge amplification on the flowcell.

And you...
Forum: Illumina/Solexa 02-08-2018, 11:54 AM
Replies: 6
Views: 495
Posted By GW_OK
But you can spike in custom primers, yeah? ...

But you can spike in custom primers, yeah?

And single read or paired-end, it doesn't really matter on the NextSeq? If it'll cluster you can just set it to do read 1.

We do single reads all the...
Forum: Illumina/Solexa 02-08-2018, 08:34 AM
Replies: 6
Views: 495
Posted By GW_OK
You mean a cBot? No, you can do single reads...

You mean a cBot?

No, you can do single reads on a NextSeq. I skimmed through the protocol and didn't see anything that made it cBot/Hiseq specific. Maybe I missed something?
Forum: Illumina/Solexa 01-09-2018, 09:42 AM
Replies: 13
Views: 1,387
Posted By GW_OK
I'll bet that's library prep costs, which is...

I'll bet that's library prep costs, which is inline with Nextera per sample costs.

Keith Robinson's saying the PE150 reagents are $625 with a 5% discount if bought in 4-packs.
Forum: Illumina/Solexa 01-09-2018, 06:51 AM
Replies: 13
Views: 1,387
Posted By GW_OK
One third of the reads for two-thirds the cost of...

One third of the reads for two-thirds the cost of a Miseq v2 kit. At least for PE150.

I really don't see the point unless they're trying to get installed in that last fraction of labs that just...
Forum: Illumina/Solexa 08-01-2017, 07:19 AM
Replies: 113
Views: 19,682
Posted By GW_OK
There've been a few hypotheses that ExAmp is...

There've been a few hypotheses that ExAmp is actually Recombinase Polymerase Amplification (RPA), developed by TwistDX.

Here's a Youtube video describing it (https://youtu.be/x6AbsOrSAoY?t=1m17s)...
Forum: Illumina/Solexa 03-28-2017, 06:55 AM
Replies: 113
Views: 19,682
Posted By GW_OK
I don't know if you can truly compare...

I don't know if you can truly compare efficiencies of the ExAmp chemistry with the other instruments.

On the HiSeq and NextSeq instruments you are randomly clustering across the flowcell with a...
Forum: Illumina/Solexa 03-20-2017, 01:39 PM
Replies: 113
Views: 19,682
Posted By GW_OK
A few more interesting points. The tile map...

A few more interesting points.

The tile map for the S2 flowcell:
-The first digit is the lane number: 1 or 2.
-The second digit represents the surface: 1 for top or 2 for bottom.
-The third...
Forum: Illumina/Solexa 03-20-2017, 08:39 AM
Replies: 113
Views: 19,682
Posted By GW_OK
Maybe we need to start talking in terms of...

Maybe we need to start talking in terms of "library coverage" instead of "genome coverage"...

Also, don't confuse read numbers with cluster numbers. There'll be 2 reads to every cluster. And on...
Forum: Illumina/Solexa 03-20-2017, 07:41 AM
Replies: 113
Views: 19,682
Posted By GW_OK
Regarding sampling depth, I am dubious. The...

Regarding sampling depth, I am dubious.

The Truseq PCR-free protocol (which I have to assume they're using) has you start with 1ug for 350bp inserts and 2ug for 550 bp inserts. Since they say...
Forum: Illumina/Solexa 03-20-2017, 06:52 AM
Replies: 113
Views: 19,682
Posted By GW_OK
It's from the BaseSpace project NovaSeq: WGS...

It's from the BaseSpace project NovaSeq: WGS TruSeq PCR-Free 450 (6plex) So I reckon it must be PCR-free.

NA12878-rep1 only looking at data from lane 1.
Forum: Illumina/Solexa 03-20-2017, 06:36 AM
Replies: 113
Views: 19,682
Posted By GW_OK
So, yeah. I didn't miss that qcfail blog post....

So, yeah. I didn't miss that qcfail blog post. I've read through it several times. I wanted to recapitulate their analysis on a data set that:
(A) had not undergone PCR amplification and
(B) was...
Forum: Illumina/Solexa 03-20-2017, 06:25 AM
Replies: 113
Views: 19,682
Posted By GW_OK
Finally, I graphed duplicate read coordinates...

Finally, I graphed duplicate read coordinates relative to the initial read coordinates (x1-x2/y1-y2 from the file I made above). I've attached that file below since it's not tremendously large. Most...
Forum: Illumina/Solexa 03-20-2017, 06:17 AM
Replies: 113
Views: 19,682
Posted By GW_OK
I then ran clumpify markduplicates=t...

I then ran clumpify markduplicates=t dupedist=2500 spantiles=t to coalesce the duplicates I used a simple perl script to parse the fastq headers into a "tile1 x1 y1 tile2 x2 y2" text...
Forum: Illumina/Solexa 03-20-2017, 06:12 AM
Replies: 113
Views: 19,682
Posted By GW_OK
The forums aren't letting me post a big post so...

The forums aren't letting me post a big post so I'm going to break this into three posts.

I've been intrigued with the question of duplicate-well directionality. Does it follow the direction of...
Forum: Illumina/Solexa 03-18-2017, 07:20 AM
Replies: 113
Views: 19,682
Posted By GW_OK
deleted due to duplication (hah)

deleted due to duplication (hah)
Forum: Illumina/Solexa 03-16-2017, 05:46 PM
Replies: 113
Views: 19,682
Posted By GW_OK
Well, since I have a 3000 (but no extant PCR-free...

Well, since I have a 3000 (but no extant PCR-free data) I wanted to look at the public 4000 data from Basespace, specifically:
NA12878-PCRfree450_S3_L003_R1_001.fastq.gz...
Forum: Illumina/Solexa 03-16-2017, 07:06 AM
Replies: 113
Views: 19,682
Posted By GW_OK
Can anyone share exactly how they're getting X/Y...

Can anyone share exactly how they're getting X/Y coordinates from the patterned flowcell fastq? I'm only seeing a single number, which I am guessing corresponds to a well ID.
Forum: Illumina/Solexa 03-14-2017, 06:37 AM
Replies: 2
Views: 848
Posted By GW_OK
2xxx tiles are on the bottom surface. I concur...

2xxx tiles are on the bottom surface. I concur with the possibilities raised by Markiyan. Looks like it started somewhere around cycle 35. Definitely a call to tech support is in order.
Forum: Illumina/Solexa 02-07-2017, 06:55 AM
Replies: 6
Views: 2,336
Posted By GW_OK
Yep. Works fine.

Yep. Works fine.
Forum: Illumina/Solexa 01-10-2017, 11:50 AM
Replies: 113
Views: 19,682
Posted By GW_OK
Eco tweeted it. And I think he was there at the...

Eco tweeted it. And I think he was there at the presentation?

Anyway, I can't find confirmation either way on the official Illumina pages.
Forum: Illumina/Solexa 10-20-2016, 08:41 AM
Replies: 13
Views: 3,839
Posted By GW_OK
One thing we have found to be helpful is to clean...

One thing we have found to be helpful is to clean up and run the qPCR products out on our Tapestation. This way you know exactly what size of product you have in your analysis.
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