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Forum: Sample Prep / Library Generation 11-30-2021, 09:47 PM
Replies: 1
Views: 175
Posted By luc
You only had three samples on the run? Thus, the...

You only had three samples on the run? Thus, the complexity of the index reads will be low and the quality of the index reads will be impacted due to extremely high fluorescence intensities in the...
Forum: Bioinformatics 10-13-2021, 07:01 PM
Replies: 4
Views: 1,367
Posted By luc
I very much agree. Thanks HESmith!

I very much agree. Thanks HESmith!
Forum: Introductions 09-29-2021, 11:50 AM
Replies: 1
Views: 761
Posted By luc
To my knowledge, your idea is supported by only...

To my knowledge, your idea is supported by only two kits, Perkin Elmer Combo-Seq and Bio-Rad SEQuoia. We have no experience with these, though.
I am not sure if the combined sequencing makes sense,...
Forum: Bioinformatics 09-29-2021, 11:22 AM
Replies: 4
Views: 1,367
Posted By luc
Sorry, I have no idea what could be happening...

Sorry, I have no idea what could be happening here. Have you checked the quality of both forward and the reverse reads with FASTQC, FASTP or similar?
Forum: Illumina/Solexa 09-24-2021, 05:19 PM
Replies: 12
Views: 10,480
Posted By luc
Me neither. The thread is very old, though....

Me neither. The thread is very old, though. Likely the attachments did get lost when the website setup was moved to a new server?
Forum: Illumina/Solexa 09-24-2021, 05:14 PM
Replies: 1
Views: 890
Posted By luc
You will not need a library prep kit. You can add...

You will not need a library prep kit. You can add all the required Illumina sequences by PCR (in one round or two rounds). This might give you an idea:...
Forum: Sample Prep / Library Generation 06-28-2021, 04:32 PM
Replies: 3
Views: 1,656
Posted By luc
It is described in detail in the Hackflex paper. ...

It is described in detail in the Hackflex paper.
The latest version of the manuscript is here: https://www.biorxiv.org/content/10.1101/779215v2
Forum: Sample Prep / Library Generation 06-28-2021, 04:26 PM
Replies: 2
Views: 1,544
Posted By luc
This seems to be 1:1 substitute for SequalPrep? ...

This seems to be 1:1 substitute for SequalPrep?
https://norgenbiotek.com/product/ngs-normalization-96-well-kit
We have no experience with it, though.
Forum: Sample Prep / Library Generation 06-24-2021, 01:13 PM
Replies: 0
Views: 1,505
Posted By luc
How does the "Illumina DNA PCR-Free Prep (Tagmentation)" work?

Has somebody here figured out how the new "Illumina DNA PCR-Free Prep (Tagmentation)" library preps work?...
Forum: Introductions 05-27-2021, 09:31 PM
Replies: 1
Views: 1,868
Posted By luc
Welcome! Don't be shy.

Welcome! Don't be shy.
Forum: RNA Sequencing 05-19-2021, 09:35 AM
Replies: 1
Views: 2,902
Posted By luc
I assume chemical fragmentation will affect the...

I assume chemical fragmentation will affect the small fragments to the same degree as the big ones.
If you have an opportunity to sonicate samples? Small fragments are pretty safe from shearing.
...
Forum: Sample Prep / Library Generation 05-04-2021, 09:17 AM
Replies: 1
Views: 1,779
Posted By luc
Demultiplexing always happens after the run. Thus...

Demultiplexing always happens after the run. Thus you can have several attempts if you have the software installed locally. Otherwise, you are relying on the aid of your core lab.

There are two...
Forum: General 04-29-2021, 04:24 PM
Replies: 2
Views: 2,566
Posted By luc
Single-cell sequencing & multi-omics forum?

Hello All,

I believe single-cell sequencing & multi-omics deserve their own forum here.
Forum: Bioinformatics 04-26-2021, 10:48 PM
Replies: 1
Views: 998
Posted By luc
You could compare your data to genetic maps and...

You could compare your data to genetic maps and find the markers in your contigs.
Forum: General 02-23-2021, 02:21 PM
Replies: 3
Views: 2,562
Posted By luc
Hi, multiple companies offer spin columns and...

Hi, multiple companies offer spin columns and spin plates.

E.g.
http://www.epochlifescience.com/Product/SpinColumn/minispin.aspx
https://bpi-tech.com/96-well-plates/

I have not used these...
Forum: Oxford Nanopore 11-30-2020, 09:45 AM
Replies: 1
Views: 3,127
Posted By luc
No remodeling needed. All Nextera libraries...

No remodeling needed.
All Nextera libraries are PCR amplified to be sequenceable. After the PCR amplification they are wonderfully double-stranded throughout and should be blunt-ended (if a...
Forum: Sample Prep / Library Generation 10-01-2020, 11:09 AM
Replies: 3
Views: 2,239
Posted By luc
You might want to have a look at this FAQ: ...

You might want to have a look at this FAQ:
https://dnatech.genomecenter.ucdavis.edu/faqs/my-pcr-free-libraries-do-not-look-as-expected-on-the-bioanalyzer-how-should-i-qc-pcr-free-libraries/
Forum: Sample Prep / Library Generation 10-01-2020, 10:57 AM
Replies: 5
Views: 2,486
Posted By luc
Depends on the dye used and the amount of...

Depends on the dye used and the amount of primers. Ethidiumbrmide is ten times less sensitive for ssDNA compared to dsDNA. The sampe seems to be true for the Bioanalyzer, but such an instrument is...
Forum: Sample Prep / Library Generation 09-26-2020, 07:39 AM
Replies: 5
Views: 2,486
Posted By luc
You could run aliquots of the reaction (before...

You could run aliquots of the reaction (before and after bead cleanups) on an agarose gel to see what is going on.
If the ligation does not work porperly, perhaps your samples have some chemical...
Forum: Sample Prep / Library Generation 09-18-2020, 12:26 AM
Replies: 5
Views: 2,450
Posted By luc
Add Qiagen UPX to the list.

Add Qiagen UPX to the list.
Forum: Sample Prep / Library Generation 09-14-2020, 11:23 PM
Replies: 5
Views: 2,450
Posted By luc
What is your goal? Gene-level studies or...

What is your goal? Gene-level studies or transcript level?
Forum: General 08-05-2020, 02:30 PM
Replies: 1
Views: 2,998
Posted By luc
One more important alternative is the Perkin...

One more important alternative is the Perkin Elmer Labchip GX Touch.
They all work and differ in the resolution, throughput, reagent costs and setup effort.
Forum: Illumina/Solexa 08-02-2020, 06:18 PM
Replies: 3
Views: 1,567
Posted By luc
I beleive there is no reason to expect the run to...

I beleive there is no reason to expect the run to fail now. The data should be usable as indicated by the qualityscores.
Forum: Illumina/Solexa 08-01-2020, 05:59 PM
Replies: 3
Views: 1,567
Posted By luc
The run is still ongoing? More information...

The run is still ongoing?
More information would be rquired.
Forum: Sample Prep / Library Generation 07-25-2020, 08:17 PM
Replies: 1
Views: 2,096
Posted By luc
Sorry, the attachments do not open for me.

Sorry, the attachments do not open for me.
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