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Forum: Illumina/Solexa 05-13-2020, 12:27 PM
Replies: 2
Views: 568
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: 4
Views: 1,134
Posted By luc
Also: bioinformatics.ucdavis.edu

Also: bioinformatics.ucdavis.edu
Forum: Illumina/Solexa 04-24-2020, 08:26 PM
Replies: 2
Views: 632
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: 802
Posted By luc
A secret tip:...

A secret tip:...
Forum: Bioinformatics 04-14-2020, 09:57 PM
Replies: 1
Views: 333
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: 516
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: 769
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: 884
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: 6,681
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: 6,681
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: 8
Views: 2,401
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: 1,351
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...
Forum: Sample Prep / Library Generation 02-04-2020, 10:09 PM
Replies: 8
Views: 2,401
Posted By luc
Hi Adam, the promised attached image seems to...

Hi Adam,
the promised attached image seems to be missing.
Forum: Bioinformatics 01-26-2020, 10:05 PM
Replies: 2
Views: 627
Posted By luc
Could you describe where your barcodes/indices...

Could you describe where your barcodes/indices are located in the Illumina reads?
In the index reads (i5 and i7) or in-line with the forward and reverse sequence reads?
Forum: Core Facilities 12-02-2019, 05:20 PM
Replies: 2
Views: 1,761
Posted By luc
What assay do you want or run with the converted...

What assay do you want or run with the converted sample?
Forum: Sample Prep / Library Generation 11-19-2019, 07:34 AM
Replies: 1
Views: 892
Posted By luc
Best ask Nugen. Likely Nugen is using the Truseq...

Best ask Nugen. Likely Nugen is using the Truseq design for their kits, not Nextera sequences.
Forum: Introductions 11-07-2019, 04:29 PM
Replies: 1
Views: 784
Posted By luc
Welcome Saba! ...

Welcome Saba!
http://kellis.blogs.ccps.us/files/2016/08/cropped-cropped-scientist-clipart-science-clip-art-school1.png
Forum: Sample Prep / Library Generation 11-07-2019, 04:24 PM
Replies: 2
Views: 1,502
Posted By luc
Not a good explanation, nevertheless: perhaps...

Not a good explanation, nevertheless: perhaps your stock of index primers is degrading or got contaminated? You might want to order a few fresh oligos and compare?
Forum: Illumina/Solexa 11-05-2019, 08:02 AM
Replies: 18
Views: 1,853
Posted By luc
This is using custom sequencing primers? The...

This is using custom sequencing primers?

The heating and cooling elements are not calibrated exactly the same for all MiSeqs (by Illumina). Some risky custom sequencing primer designs can work...
Forum: Introductions 11-04-2019, 07:18 PM
Replies: 1
Views: 794
Posted By luc
Well ........ welcome Tom! ...

Well ........ welcome Tom!

https://images-na.ssl-images-amazon.com/images/S/sgp-catalog-images/region_US/wb-883316329542-Full-Image_GalleryBackground-en-US-1484348613962._SX1080_.jpg
Forum: Sample Prep / Library Generation 10-30-2019, 03:34 PM
Replies: 2
Views: 1,205
Posted By luc
Yep, bead cleanups will never be perfect. You can...

Yep, bead cleanups will never be perfect. You can only enrich for molecules of the desired size range.
Many protocols suggest two rounds of bead cleanups likey to safeguard for less than optimal...
Forum: Sample Prep / Library Generation 10-08-2019, 05:18 PM
Replies: 10
Views: 1,606
Posted By luc
It will. Who says molecular...

It will.

Who says molecular physics/chemistry is easy? These signals are likely due to the nature of dyes. Likely the HS-DNA dye will mostly bind to dsDNA to become fluorescent, but also to...
Forum: Sample Prep / Library Generation 10-03-2019, 11:08 AM
Replies: 10
Views: 1,606
Posted By luc
I guess your RNA coul actually be clean, DNA-free.

I guess your RNA coul actually be clean, DNA-free.
Forum: Sample Prep / Library Generation 10-03-2019, 08:21 AM
Replies: 10
Views: 1,606
Posted By luc
Qubit DNA assays will also measure Doublestranded...

Qubit DNA assays will also measure Doublestranded RNA, e.g. ds parts of rRNA.
Do you see any signs of DNA on the Bioanalyzer?
Forum: Sample Prep / Library Generation 09-11-2019, 04:19 PM
Replies: 1
Views: 1,292
Posted By luc
I am not aware of such a protocol. Best sequence...

I am not aware of such a protocol. Best sequence the library to low coverage as a spike-in into another run first - using different barcodes obviously.
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