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Search: Posts Made By: luc
Forum: Sample Prep / Library Generation 11-06-2018, 11:36 PM
Replies: 2
Views: 555
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: 609
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: 611
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: 514
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: 1,180
Posted By luc
Thanks for the links!

Thanks for the links!
Forum: General 09-30-2018, 10:07 PM
Replies: 13
Views: 1,180
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: 819
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: 2,151
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...
Forum: Illumina/Solexa 08-01-2018, 12:55 PM
Replies: 11
Views: 1,383
Posted By luc
I would certainly filter the reads based on...

I would certainly filter the reads based on average quality scores (not losing more than
15 % of the reads) and do some very gentle quality trimming from the 3' end.
Forum: Sample Prep / Library Generation 07-31-2018, 05:45 PM
Replies: 2
Views: 967
Posted By luc
We have not tried it, but it looks promising for...

We have not tried it, but it looks promising for for very large projects - meaning hundreds of samples?
Forum: Illumina/Solexa 07-31-2018, 04:39 PM
Replies: 11
Views: 1,383
Posted By luc
Yes, this is certainly correct. However,...

Yes, this is certainly correct. However, RNA-seq libraries generated with most protocols have a strong bias towards smaller fragments - in contrast to genomic libraries. Please see the attached...
Forum: Illumina/Solexa 07-31-2018, 04:31 PM
Replies: 1
Views: 726
Posted By luc
It should not cluster at all. Please let us know...

It should not cluster at all. Please let us know in case you witness a miracle.
Forum: Illumina/Solexa 07-30-2018, 08:53 PM
Replies: 11
Views: 1,383
Posted By luc
Hi pecanton, this is a subset of the data?...

Hi pecanton,

this is a subset of the data? How many reads did you get in total?
There was indeed an issue with the flowcell, localized low quality regions causing the low quality data. Likely...
Forum: Illumina/Solexa 07-16-2018, 08:04 PM
Replies: 4
Views: 986
Posted By luc
You have seen this info from Illumina:...

You have seen this info from Illumina:...
Forum: RNA Sequencing 07-13-2018, 06:53 PM
Replies: 1
Views: 972
Posted By luc
Prolonged high heat exposure definitely...

Prolonged high heat exposure definitely introduces a lot of damages to DNA. I would expect it to be pretty fragmented by now. I also assume the Nextera transpose would require dsDNA - thus, you...
Forum: Sample Prep / Library Generation 06-16-2018, 07:08 PM
Replies: 3
Views: 950
Posted By luc
Give it more time and vortex once in a while. ...

Give it more time and vortex once in a while. They will resuspend in the end.
Forum: Bioinformatics 06-15-2018, 06:16 PM
Replies: 1
Views: 497
Posted By luc
An DNA oligo with a rGrGrG 3'-end ((the template...

An DNA oligo with a rGrGrG 3'-end ((the template switching oligo) will anneal to the CCC overhang and the RT will continue to work on this newly added template. This allows you to add a defined...
Forum: Ion Torrent 06-15-2018, 06:09 PM
Replies: 3
Views: 1,327
Posted By luc
A neighboring lab has the OT-One. This first...

A neighboring lab has the OT-One. This first version is unusable for just about anything - it can't hold the pipettes properly and the plates have a lot of play. Version two looks very different,...
Forum: Illumina/Solexa 05-31-2018, 06:08 PM
Replies: 1
Views: 510
Posted By luc
Is this a one-off experiment or are you planning...

Is this a one-off experiment or are you planning for multiple samples?

You will need to shear the DNA sample either by sonication or enzymatically to pieces of about 300 to 450 bp length for the...
Forum: Bioinformatics 04-22-2018, 03:16 PM
Replies: 13
Views: 1,640
Posted By luc
Final costs depend on reagent costs and yields...

Final costs depend on reagent costs and yields (and reliability). Results for both systems will depend a lot on DNA sample quality. At current yields the Sequel runs will yield more data/dollar in...
Forum: Bioinformatics 04-20-2018, 05:16 PM
Replies: 13
Views: 1,640
Posted By luc
The sequencer is certainly cheap, but to my...

The sequencer is certainly cheap, but to my knowledge not the reagents and additional flowcells. PacBio might be more affordable?
Forum: Illumina/Solexa 04-13-2018, 07:01 PM
Replies: 2
Views: 891
Posted By luc
It could work - however you will not be able to...

It could work - however you will not be able to sue the PhiX libraries as spike in since you will can't use the Illumina sequencing primers together with your extended versions.
Forum: Bioinformatics 04-06-2018, 04:23 PM
Replies: 658
Views: 139,979
Posted By luc
Convenient way to avoid re-indexing references? ...

Convenient way to avoid re-indexing references?

When working with big genomes one would really like to avoid re-indexing reference sequences. BBmap is always looking for the reference indices in...
Forum: Sample Prep / Library Generation 03-31-2018, 11:22 AM
Replies: 5
Views: 1,526
Posted By luc
It is unlikely that the Tn5 will cut/tagment your...

It is unlikely that the Tn5 will cut/tagment your 113 bp fragment twice - this would be required for sequencing.
Forum: Sample Prep / Library Generation 03-26-2018, 06:58 PM
Replies: 1
Views: 831
Posted By luc
The NEBNext® End Repair Module is missing the...

The NEBNext® End Repair Module is missing the A-tailing component (likely taq ploymerase).
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