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Search: Posts Made By: luc
Forum: Sample Prep / Library Generation Yesterday, 11:31 PM
Replies: 4
Views: 163
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 Yesterday, 11:25 PM
Replies: 3
Views: 157
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: 133
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: 590
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: 645
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: 650
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: 529
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: 1,228
Posted By luc
Thanks for the links!

Thanks for the links!
Forum: General 09-30-2018, 10:07 PM
Replies: 13
Views: 1,228
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: 843
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: 2,185
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: 1,400
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: 983
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: 1,400
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: 746
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: 1,400
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: 1,001
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: 978
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: 958
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: 505
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: 1,375
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: 515
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: 1,668
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: 1,668
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: 906
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.
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