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Forum: Illumina/Solexa 07-23-2015, 03:44 AM
Replies: 6
Views: 2,150
Posted By andibody
Thanks for the link!

Thanks for the link!
Forum: Illumina/Solexa 07-23-2015, 03:20 AM
Replies: 6
Views: 2,150
Posted By andibody
If the size bias is so extreme, does it mean that...

If the size bias is so extreme, does it mean that applications with non-random insert sizes shouldn't be run on the HiSeq3000/4000 at all?
Forum: Illumina/Solexa 07-22-2015, 06:45 AM
Replies: 6
Views: 2,150
Posted By andibody
I heard fragments from 400bp on or even below...

I heard fragments from 400bp on or even below would start causing problems?
Forum: Illumina/Solexa 01-26-2015, 01:01 AM
Replies: 53
Views: 60,982
Posted By andibody
High Output. True, it's more like 270-290M with...

High Output.
True, it's more like 270-290M with Q>30.
Still, it's 'only' a 15% increase. (again, not countering in speed and evenness of cluster density).
Forum: Illumina/Solexa 01-25-2015, 09:43 AM
Replies: 53
Views: 60,982
Posted By andibody
There should be an exact max of clusters for...

There should be an exact max of clusters for HiSeq 3000/4000 defined by the number of microwells (325M as stated above?).
We're getting regularly 300M reads on the upgraded 2500. If 325M is correct,...
Forum: Illumina/Solexa 01-22-2015, 11:47 PM
Replies: 53
Views: 60,982
Posted By andibody
Our sales rep claimed there are no single read...

Our sales rep claimed there are no single read cluster kits available (yet) for HS3000/4000. Can anyone confirm? Sounds like a strange decision (if true) to me.
Forum: Core Facilities 09-26-2014, 03:06 AM
Replies: 1
Views: 2,178
Posted By andibody
Can they be upgraded or do they have the old...

Can they be upgraded or do they have the old camera built in?

Best
Forum: Illumina/Solexa 12-04-2013, 02:15 AM
Replies: 18
Views: 6,888
Posted By andibody
Our local sales representative just explained...

Our local sales representative just explained that the 2x250 upgrade is independent from the 1Tb upgrade.
One of our HiSeqs was upgraded this year to 2500 but it seems that the camera is still too...
Forum: Illumina/Solexa 07-04-2013, 12:57 AM
Replies: 9
Views: 2,712
Posted By andibody
The last picture reminds me of problems we had...

The last picture reminds me of problems we had with the mode scrambler.
Forum: Sample Prep / Library Generation 02-18-2013, 12:49 AM
Replies: 3
Views: 994
Posted By andibody
Arabidopsis whole genome DNA.

Arabidopsis whole genome DNA.
Forum: Sample Prep / Library Generation 02-13-2013, 03:31 AM
Replies: 3
Views: 994
Posted By andibody
Cheapest 96 well WGS sample prep

Hi,

Has anybody tried to minimize sample prep costs (for Illumina sequencing) in 96 well format? How low have you got and using which reagents?
We want to sequence >20k samples and while heavily...
Forum: Sample Prep / Library Generation 02-28-2012, 03:06 AM
Replies: 1
Views: 1,113
Posted By andibody
Bioanalyzer peak at 107bp

Hi,
we're getting a narrow single peak at 107bp after size selection on gel and subsequent PCR.
Apart from that, bioanalyzer profiles of the libraries look fine.
I'm pretty sure there have been...
Forum: Illumina/Solexa 11-22-2011, 08:46 AM
Replies: 15
Views: 4,963
Posted By andibody
Great, thanks a lot, that's exactly what I wanted...

Great, thanks a lot, that's exactly what I wanted to know.

Best Wishes
Andi
Forum: Illumina/Solexa 11-22-2011, 06:43 AM
Replies: 15
Views: 4,963
Posted By andibody
We had to fill up a PE flowcell and took...

We had to fill up a PE flowcell and took therefore this SR library (small RNA adapters no Truseq).
It didn't really work, very few, very small clusters. I was expecting to get the first read only...
Forum: Illumina/Solexa 11-21-2011, 07:06 AM
Replies: 15
Views: 4,963
Posted By andibody
Thanks for your comment but I haven't found the...

Thanks for your comment but I haven't found the exact answer I'm looking for.
I know single read adapters can not be used for paired end sequencing, the question is if I get only one read or if...
Forum: Illumina/Solexa 11-21-2011, 03:06 AM
Replies: 15
Views: 4,963
Posted By andibody
SR Adapters on a PE flowcell?

Does this work? Of course only for the first read...
Or do you think colony formation will not work at all?

Thanks
Forum: Sample Prep / Library Generation 08-10-2011, 08:17 AM
Replies: 2
Views: 13,868
Posted By andibody
Thanks a lot for the link! So, are you going to...

Thanks a lot for the link!
So, are you going to try the low-level pooling experiments?
Interesting protocol, just had a quick look but I'm looking forward to hear how it worked.
From time to time...
Forum: Sample Prep / Library Generation 08-10-2011, 07:45 AM
Replies: 2
Views: 13,868
Posted By andibody
Truseq Multiplexing / Minimal number of Samples

Hi,

we have been working for a while with custom barcoded adapters. Successful basecalling seems to depend mostly on sufficient base complexity and we therefore run a minimum of 4 samples per...
Forum: Pacific Biosciences 05-10-2011, 07:22 AM
Replies: 1
Views: 2,713
Posted By andibody
Hands on experience someone?

Hi,

I have still only little information on how PacBio's system is performing. Anyone here who could share some experiences?

Best
AB
Forum: Illumina/Solexa 09-25-2010, 04:54 AM
Replies: 7
Views: 4,169
Posted By andibody
peaks of bianalyzer result seem small, wouldn't...

peaks of bianalyzer result seem small, wouldn't you expects lots of material if template DNA was abundant?
(I suppose 1 ul was used for quantification)
Forum: Illumina/Solexa 09-25-2010, 04:18 AM
Replies: 7
Views: 4,169
Posted By andibody
Nextera says bird-nesting isn't a problem: ...

Nextera says bird-nesting isn't a problem:
"After the Nextera tagmentation reaction and PCR, you may notice an apparent fragment size of 500 bases (or greater) when the DNA is analyzed on an Agilent...
Forum: Illumina/Solexa 09-23-2010, 07:33 AM
Replies: 7
Views: 1,786
Posted By andibody
no, the density problems were observed even on...

no, the density problems were observed even on whole genome samples.
Forum: Illumina/Solexa 09-23-2010, 07:24 AM
Replies: 7
Views: 4,169
Posted By andibody
we too see it happen from time to time but we...

we too see it happen from time to time but we haven't been able to nail it down to specific conditions. hope we get more input from other users.
Forum: Illumina/Solexa 09-14-2010, 01:28 AM
Replies: 7
Views: 1,786
Posted By andibody
Indeed, it started happening after we upgraded...

Indeed, it started happening after we upgraded the software. Could it be that the new image analysis resolves more clusters but at the same time is less unforgivable to high cluster density?...
Forum: Illumina/Solexa 09-09-2010, 05:16 AM
Replies: 7
Views: 1,786
Posted By andibody
Erratic cluster numbers

Hi,

Since ~ 2 months we are getting erratic cluster numbers on our GAs (cBot) even if we check the libraries with RT-PCR. Before we were using 7pM (~300.000clusters /tile) and were getting...
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