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Search: Posts Made By: luc
Forum: Illumina/Solexa 02-18-2019, 09:25 AM
Replies: 1
Views: 132
Posted By luc
The results do vary by sequencer (the Hiseq 4000...

The results do vary by sequencer (the Hiseq 4000 is not - or only minimally - bothered by dual matched indices); the NovaSeq OTOH can tank with these. Likely library insert sizes can also play a...
Forum: RNA Sequencing 02-14-2019, 11:14 PM
Replies: 1
Views: 140
Posted By luc
How do you know? I would suggest to follow the...

How do you know? I would suggest to follow the library prep protocol all the way to the end and then assess the library or lack thereof.
Forum: Illumina/Solexa 02-07-2019, 06:16 PM
Replies: 1
Views: 204
Posted By luc
PCR-free Y-adapter libraries can migrate in funky...

PCR-free Y-adapter libraries can migrate in funky ways and can hide adapter dimers. In short they are difficult to QC.
I would suggest a diagnostic PCR with a small aliquot of the libraries:...
Forum: Introductions 01-24-2019, 06:19 PM
Replies: 2
Views: 651
Posted By luc
Hi msharik, A big hello to Indore: ...

Hi msharik,

A big hello to Indore: https://en.wikipedia.org/wiki/Indore
Forum: Sample Prep / Library Generation 01-21-2019, 09:14 AM
Replies: 0
Views: 400
Posted By luc
"random" enzymatic DNA fragmentation - how does it work?

Hi All,

almost all sequencing library preparation kit providers now offer kits promising "random" enzymatic DNA fragmentation that are not based on transposon tagmentation - adapters are ligated...
Forum: Core Facilities 01-19-2019, 06:26 PM
Replies: 3
Views: 587
Posted By luc
Bukowski is correct. RNA-seq library prep...

Bukowski is correct. RNA-seq library prep protocols (starting from RNA) are optimized for consistency to allow quantitative DGE analysis. Your cDNA prep protocol might not be.
Is your cDNA...
Forum: Sample Prep / Library Generation 01-14-2019, 08:51 AM
Replies: 15
Views: 13,535
Posted By luc
Yep, the enzymatic fragmentation products...

Yep, the enzymatic fragmentation products generated by kits from from several vendors do not require any end-repair.
Forum: 454 Pyrosequencing 01-14-2019, 08:46 AM
Replies: 5
Views: 4,900
Posted By luc
In the age of long read sequencing (PacBio,...

In the age of long read sequencing (PacBio, Nanopore) and linked reads (10X Genomics), "mate pair" sequencing is as obsolete as 454.
Forum: Sample Prep / Library Generation 01-11-2019, 03:46 PM
Replies: 3
Views: 513
Posted By luc
Nextflex adapters are available for DNA...

Nextflex adapters are available for DNA applications and for RNA-seq applications. The latter are merely dilutions of the former, but Bioo provides the concentration info somewhere.
If you have...
Forum: Sample Prep / Library Generation 01-10-2019, 09:59 PM
Replies: 3
Views: 513
Posted By luc
Check the concentration of the Nextflex RNA-seq...

Check the concentration of the Nextflex RNA-seq adapters on their web page; I have not memorized it but it will work.
Forum: Pacific Biosciences 01-07-2019, 06:03 PM
Replies: 5
Views: 767
Posted By luc
Nothing about the read metrics raises warning...

Nothing about the read metrics raises warning flags - they could certainly have generated longer library molecules though since they did not multiplex the library.

Is the genome size about what...
Forum: Illumina/Solexa 12-29-2018, 01:39 PM
Replies: 9
Views: 1,391
Posted By luc
I would suggest to check the index reads for this...

I would suggest to check the index reads for this particular library to see which base is affected.
Forum: General 12-24-2018, 12:44 PM
Replies: 3
Views: 724
Posted By luc
Hi Kujin, to my knowledge the Lohman...

Hi Kujin,

to my knowledge the Lohman protocol should work, as is, on the iSeq - as any other Truseq library design. We do not have an iSeq however. Do you want to optimize it for paired-end...
Forum: General 12-20-2018, 09:24 PM
Replies: 3
Views: 724
Posted By luc
Could you point us to your complete protocol? ...

Could you point us to your complete protocol? There are multiple Tag-seq protocols out there.
Likely your first amplification was already failing.
Your PCR cycles shows two consecutive stages at...
Forum: Sample Prep / Library Generation 12-17-2018, 11:31 PM
Replies: 4
Views: 573
Posted By luc
Randomprimer-dimers will be basically unavoidable...

Randomprimer-dimers will be basically unavoidable for your low, unmeasurable input.
If the oligos are a separate reagent, you could try to reduce their concentration.
Forum: Bioinformatics 12-17-2018, 11:25 PM
Replies: 3
Views: 482
Posted By luc
bcl2fastq will only transfer the UMI information...

bcl2fastq will only transfer the UMI information into the read header and trim them out of the reads as an option - nothing else.
UMI-tools are more sophisticated and have many additional functions.
Forum: Illumina/Solexa 12-12-2018, 06:11 PM
Replies: 1
Views: 488
Posted By luc
Did you use custom sequencing primers for any of...

Did you use custom sequencing primers for any of the reads?
Forum: Sample Prep / Library Generation 11-06-2018, 11:36 PM
Replies: 2
Views: 811
Posted By luc
Both column kits and SPRI beads will work just...

Both column kits and SPRI beads will work just fine. Beads make it easier to work with multiple samples in parallel. Almost "All" manufacturers are now selling SPRI beads. I would bet they all work...
Forum: Illumina/Solexa 10-13-2018, 11:05 AM
Replies: 2
Views: 738
Posted By luc
As long as the short library molecules are a...

As long as the short library molecules are a smaller fraction of the loaded libraries (<20%?) there will be no problem.
Forum: Illumina/Solexa 10-10-2018, 10:30 PM
Replies: 1
Views: 759
Posted By luc
You are correct about the truseq style adapters....

You are correct about the truseq style adapters. Sorry I do not know about additional documentation.
Forum: Illumina/Solexa 10-08-2018, 05:50 PM
Replies: 1
Views: 616
Posted By luc
To be able to add single-T-tailed adapters like...

To be able to add single-T-tailed adapters like the Illumina Truseq adapters via ligation. This is a way to prevent (or strongly reduce) insert-to-insert ligation and adapter-to-adapter ligation.
Forum: General 10-03-2018, 11:30 AM
Replies: 13
Views: 1,919
Posted By luc
Thanks for the links!

Thanks for the links!
Forum: General 09-30-2018, 10:07 PM
Replies: 13
Views: 1,919
Posted By luc
I am not working in this field, but to me these...

I am not working in this field, but to me these ideas have some charm. I am curious about any supporting data.
Forum: Illumina/Solexa 08-05-2018, 04:46 PM
Replies: 2
Views: 987
Posted By luc
The 5' bias is mostly due to the A-tailing...

The 5' bias is mostly due to the A-tailing reaction.
Forum: Metagenomics 08-02-2018, 05:30 PM
Replies: 2
Views: 2,491
Posted By luc
What type of results do you have at the moment? ...

What type of results do you have at the moment?

I am sure there will be a way to generate heatmaps in Excel.

It will certainly better in the long run to become familiar with R/RStudio and the...
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