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Forum: Sample Prep / Library Generation Today, 06:39 AM
Replies: 1
Views: 169
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 09-17-2020, 11:26 PM
Replies: 5
Views: 936
Posted By luc
Add Qiagen UPX to the list.

Add Qiagen UPX to the list.
Forum: Sample Prep / Library Generation 09-14-2020, 10:23 PM
Replies: 5
Views: 936
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, 01:30 PM
Replies: 1
Views: 978
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, 05:18 PM
Replies: 3
Views: 542
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, 04:59 PM
Replies: 3
Views: 542
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, 07:17 PM
Replies: 1
Views: 779
Posted By luc
Sorry, the attachments do not open for me.

Sorry, the attachments do not open for me.
Forum: Oxford Nanopore 07-24-2020, 11:53 AM
Replies: 6
Views: 2,416
Posted By luc
In our experience the ligation and associated...

In our experience the ligation and associated reagents is the most sensitive part of library preps. I would expect other reagents to last longer past the expiration date, but I won't make any...
Forum: Illumina/Solexa 07-23-2020, 05:15 PM
Replies: 1
Views: 787
Posted By luc
Yes, you definitely want to QC your library for...

Yes, you definitely want to QC your library for the fragment lengths before sequencing using a Bioanalyzer or equivalent devices.
Forum: Introductions 07-23-2020, 05:09 PM
Replies: 1
Views: 739
Posted By luc
Cogito ergo seq. Welcome

Cogito ergo seq.

Welcome
Forum: Oxford Nanopore 07-22-2020, 01:26 PM
Replies: 6
Views: 2,416
Posted By luc
Three months should not make a meaningful...

Three months should not make a meaningful difference with these reagents - if they were stored properly.
Forum: Bioinformatics 06-18-2020, 08:18 PM
Replies: 1
Views: 1,085
Posted By luc
For a plant or an animal?

For a plant or an animal?
Forum: Sample Prep / Library Generation 06-05-2020, 05:20 PM
Replies: 1
Views: 1,396
Posted By luc
I have never seen any problems with DNA samples...

I have never seen any problems with DNA samples in EBT or EB buffer.
This tiny amount of detergent does not seem to cause problems.
I agree with avoiding EDTA buffers;at least at 1 mM...
Forum: Illumina/Solexa 05-13-2020, 12:27 PM
Replies: 2
Views: 1,416
Posted By luc
Could you let us know what specific problems you...

Could you let us know what specific problems you see with the data (and the DNA samples?)?
Forum: Introductions 04-28-2020, 12:55 PM
Replies: 5
Views: 2,008
Posted By luc
Also: bioinformatics.ucdavis.edu

Also: bioinformatics.ucdavis.edu
Forum: Illumina/Solexa 04-24-2020, 08:26 PM
Replies: 2
Views: 1,378
Posted By luc
Who is advertising this? Hard to tell what it...

Who is advertising this?
Hard to tell what it means - there are soo many different library prep chemistry options.
Forum: Sample Prep / Library Generation 04-16-2020, 03:20 PM
Replies: 6
Views: 1,612
Posted By luc
A secret tip:...

A secret tip:...
Forum: Bioinformatics 04-14-2020, 09:57 PM
Replies: 1
Views: 562
Posted By luc
Very likely the ONT data are not suitable for the...

Very likely the ONT data are not suitable for the kmer analysis. The read error rate is likely too high. Every 27 nt stretch can be expected to contain errors?

This will work with Illumina or HiFi...
Forum: Sample Prep / Library Generation 03-31-2020, 06:50 PM
Replies: 3
Views: 1,379
Posted By luc
Thanks!!! This is a neat idea.

Thanks!!!
This is a neat idea.
Forum: Illumina/Solexa 03-05-2020, 03:40 PM
Replies: 2
Views: 1,210
Posted By luc
This is expected. You are sequencing through the...

This is expected. You are sequencing through the poly-A tail. You can ignore this part of the data, and sequence only ~30 (?) cycles for the forward read next time.
Forum: Sample Prep / Library Generation 02-06-2020, 08:22 PM
Replies: 1
Views: 1,331
Posted By luc
I believe you can use standard barcoded Nextera...

I believe you can use standard barcoded Nextera primers instead. Preferentially UDI dual indexed versions of the Nextera primers.
Simple desalted oligos will be fine indeed.
Forum: Sample Prep / Library Generation 02-06-2020, 08:09 PM
Replies: 21
Views: 7,689
Posted By luc
Thanks. No manual available yet. List price is...

Thanks. No manual available yet. List price is $82 per reaction.
Forum: Sample Prep / Library Generation 02-05-2020, 06:00 PM
Replies: 21
Views: 7,689
Posted By luc
According to rumors, RiboZero will make a...

According to rumors, RiboZero will make a comeback. Not exactly the same products though; it will use a new chemistry.
Forum: Sample Prep / Library Generation 02-05-2020, 05:53 PM
Replies: 9
Views: 3,489
Posted By luc
Thanks Adam, this image is very helpful!

Thanks Adam,
this image is very helpful!
Forum: General 02-04-2020, 10:21 PM
Replies: 1
Views: 1,957
Posted By luc
To me the data you mentioned are no big reason to...

To me the data you mentioned are no big reason to worry. They gave you more data for the first sample, but duplicates are certianly higher than expected.
The biases visible for the first 16 nt in...
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