SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 324
Search took 0.01 seconds.
Search: Posts Made By: luc
Forum: Bioinformatics 04-22-2018, 02:16 PM
Replies: 13
Views: 1,362
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, 04:16 PM
Replies: 13
Views: 1,362
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, 06:01 PM
Replies: 2
Views: 554
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, 03:23 PM
Replies: 636
Views: 121,566
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, 10:22 AM
Replies: 5
Views: 1,143
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, 05:58 PM
Replies: 1
Views: 629
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).
Forum: Illumina/Solexa 01-16-2018, 03:55 PM
Replies: 29
Views: 5,503
Posted By luc
Hi ngagnes, in our experience the reagent...

Hi ngagnes,

in our experience the reagent quality has gotten better, but is still not as good as 3 years ago and we still see our low quality run outliers (that should have performed better...
Forum: Illumina/Solexa 01-10-2018, 11:55 AM
Replies: 13
Views: 1,809
Posted By luc
I guess the libraries are the same as for the...

I guess the libraries are the same as for the other Illumina sequencers?
Forum: Sample Prep / Library Generation 01-09-2018, 04:31 PM
Replies: 0
Views: 504
Posted By luc
AmpliSeq - what makes it special?

Hi All,

I might be a bit dense. Could you help me understand what makes the AmpliSeq protocol special?


It seems to use multiplexed PCR primers with universal tags.
These universal tags...
Forum: Illumina/Solexa 01-09-2018, 04:17 PM
Replies: 3
Views: 453
Posted By luc
Hi liaoyunshi, sorry, I do not understand...

Hi liaoyunshi,

sorry, I do not understand what you are trying to achieve with the inline barcodes.
Working with the tru-seq style barcodes is preferable for all applications I can think off.
...
Forum: Illumina/Solexa 01-09-2018, 08:44 AM
Replies: 13
Views: 1,809
Posted By luc
This has more details: ...

This has more details:
http://omicsomics.blogspot.com/2018/01/iseq.html#more

If the flowcell price is correct it seems that the instrument is currently only of interest in cases where speed is of...
Forum: Illumina/Solexa 01-09-2018, 08:26 AM
Replies: 13
Views: 1,809
Posted By luc
I guess the low instrument cost and the small...

I guess the low instrument cost and the small size are supposed to sway people who are impressed by the nanopore instruments? despite the data being of completely different nature.
I twill totally...
Forum: Illumina/Solexa 01-08-2018, 07:19 PM
Replies: 3
Views: 453
Posted By luc
Hi liaoyunshi, Adding inline barcodes by...

Hi liaoyunshi,
Adding inline barcodes by ligation requires more effort (synthesis of two partially complementary oligos for each barcode) than adding truseq-style barcodes. Is there a special...
Forum: Illumina/Solexa 12-29-2017, 09:06 AM
Replies: 20
Views: 12,413
Posted By luc
As mentioned above, the two peaks could very well...

As mentioned above, the two peaks could very well be a sign of a mixed sample (contamination).
You could remove the all the high GC content reads and see if this improves the assembly.
BBtools...
Forum: Bioinformatics 12-26-2017, 01:27 PM
Replies: 3
Views: 1,181
Posted By luc
Anybody looking at this would need some more...

Anybody looking at this would need some more info: What type of organism? Which genome size is expected? What read lengths did you use? What library prep protocol and insert sizes?
Forum: Sample Prep / Library Generation 12-22-2017, 04:42 PM
Replies: 4
Views: 1,511
Posted By luc
I have not done any tests. I guess the assumption...

I have not done any tests. I guess the assumption is that the oligos will make multiple attempts to hybridize and that a two-base anchor is "stronger" than a single base.
Forum: Sample Prep / Library Generation 11-22-2017, 05:44 PM
Replies: 4
Views: 880
Posted By luc
As consequence from what Eric wrote, one often...

As consequence from what Eric wrote, one often has to eyeball the RNA integrity for insect samples on the Bioanalyzer (I am looking ratio of the rRNA peak size to the smaller debris fragments).
Your...
Forum: Sample Prep / Library Generation 11-22-2017, 03:35 PM
Replies: 5
Views: 1,784
Posted By luc
Yep, we have been using MagBio's HighPrep PCR...

Yep, we have been using MagBio's HighPrep PCR beads and the KapaPure beads. Both worked similar to the Ampure XP beads, also for size selections.
Forum: Pacific Biosciences 11-22-2017, 03:29 PM
Replies: 4
Views: 992
Posted By luc
Markiyan has alluded to it already; Pacbio data...

Markiyan has alluded to it already; Pacbio data are not suitable for genome size estimates based on kmer analyses. The error rates of the uncorrected raw data are too high.
Forum: RNA Sequencing 11-03-2017, 12:42 AM
Replies: 4
Views: 1,283
Posted By luc
Thanks Joseph! Have you perhaps tried...

Thanks Joseph!
Have you perhaps tried extending the UMI a bit?
Forum: Sample Prep / Library Generation 11-03-2017, 12:36 AM
Replies: 2
Views: 665
Posted By luc
The sequences of Kapa, TrueSeq and...

The sequences of Kapa, TrueSeq and BiooScientific adapters are identical, except perhaps some index sequences. They are compatible, you might have to figure out the appropriate concentrations.
Forum: RNA Sequencing 11-02-2017, 05:00 AM
Replies: 4
Views: 1,283
Posted By luc
Thanks for the information Joseph, I would...

Thanks for the information Joseph,

I would have two questions:
Why should the Smart oligos be 5' biotinylated?
How much of a balanced library do you need to spike in to sequence through the...
Forum: Pacific Biosciences 10-31-2017, 11:50 PM
Replies: 4
Views: 947
Posted By luc
10 to13 kb libraries sounds a bit short? Which...

10 to13 kb libraries sounds a bit short? Which length were the samples sheared for and which cut did you use for the pippin sise-selection?
Forum: Illumina/Solexa 10-23-2017, 10:11 PM
Replies: 15
Views: 6,084
Posted By luc
The HiSeq 4000 works now quite well with low...

The HiSeq 4000 works now quite well with low complexity libraries. There was a software update about a year ago.
Forum: Illumina/Solexa 10-11-2017, 03:57 PM
Replies: 26
Views: 3,834
Posted By luc
I am not sure that index hopping onto PhiX reads...

I am not sure that index hopping onto PhiX reads would be a good measure. As far as I remember the Illumina PhiX adapter sequences are quite different from TruSeq or Nextera sequences.
Showing results 1 to 25 of 324

 


All times are GMT -8. The time now is 07:15 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO