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Forum: Pacific Biosciences 04-05-2017, 02:14 AM
Replies: 2
Views: 1,629
Posted By BioGenomics
thanks rhall, indeed, running LAA per...

thanks rhall,

indeed, running LAA per amplicon was an idea we had as well, the whitelist will then increase analysis speed ! We'll give it a go soon.

If any other tool available for the the...
Forum: Pacific Biosciences 04-04-2017, 05:38 AM
Replies: 2
Views: 1,629
Posted By BioGenomics
Question Haplotyping/genotyping tool PacBio?

Hi all,

we have data from 40 different amplicons of different sizes (400 - 4000 bp) that have various coverage levels sequenced in a plant, hence LAA struggles with this dataset (clustering...
Forum: Sample Prep / Library Generation 01-17-2017, 01:23 AM
Replies: 1
Views: 1,708
Posted By BioGenomics
Question ddRAD/GBS lib conc on HiSeq 3000/4000 ?

Hi all,

Has anybody any advice on the "best" concentration (pM) to load a ddRAD or GBS libraries on a HiSeq 3000/4000 ? ddRAD have 300-600 bp, while GBS more around 250-350 bp lib sizes. I know...
Forum: Metagenomics 12-02-2016, 01:20 PM
Replies: 4
Views: 4,106
Posted By BioGenomics
Miseq Reporter Metagenomics and summary

Hi all,

here is some info on Illumina's read classifier for metagenomics:...
Forum: Metagenomics 11-18-2016, 03:26 AM
Replies: 19
Views: 7,288
Posted By BioGenomics
Hi all, what is the minimum Q-value you...

Hi all,

what is the minimum Q-value you would suggest for a 16s read/merged amplicon Trimming/clipping ?

thanks
Forum: Sample Prep / Library Generation 01-27-2015, 11:29 PM
Replies: 0
Views: 1,763
Posted By BioGenomics
Robotics Workstation: Sciclone NGSx vs QIAGEN suite

Hi,

We are looking into buying a robotics workstation system to perform high-throughput DNA/RNA extractions, but also preferably downstream NGS library preps.

I would be happy to hear anybody...
Forum: Sample Prep / Library Generation 01-13-2015, 08:59 PM
Replies: 6
Views: 3,451
Posted By BioGenomics
Looks promising indeed, how does this lib prep...

Looks promising indeed, how does this lib prep compare to the NEB Ultra DNA kit for instance ? Did you use it already ? Pricing ?
Forum: Sample Prep / Library Generation 01-13-2015, 05:57 PM
Replies: 6
Views: 3,451
Posted By BioGenomics
Thanks nucacidhunter. Well as I don't have an...

Thanks nucacidhunter. Well as I don't have an extensive list of SNPs for my species (some RAD data, but no good flanking regions... I might try a capture method as there is a draft genome (set of...
Forum: Sample Prep / Library Generation 01-12-2015, 07:51 PM
Replies: 6
Views: 3,451
Posted By BioGenomics
NGS library prep method for RRS/GBS/RADseq of degraded/ancient DNA?

Hi,

I am looking for the best NGS library prep method for RRS/GBS/RAD sequencing of degraded/low/template/ancient DNA ? Any good protocol available to genotype 5-10K SNPs in 100-200 inds reliably...
Forum: Genomic Resequencing 01-07-2015, 08:58 PM
Replies: 0
Views: 2,169
Posted By BioGenomics
Question Best alternative for Nextera Indices for multiple amplicon resequencing experiment ?

Hi all,

after using the 96 plex double indexing kit (8 X 12 indices) of Illumina for 16s studies, we now apply this for other amplicon resequencing purposes. But as expected this is a quite...
Forum: Epigenetics 12-02-2014, 09:34 PM
Replies: 1
Views: 1,801
Posted By BioGenomics
Hi all, Still looking for feedback whether...

Hi all,

Still looking for feedback whether or not we should go on with the faint smear seen on the gels (we started with 0.25 ng/ul bacterial ChipEd DNA)

thanks
Forum: Epigenetics 11-30-2014, 07:48 PM
Replies: 1
Views: 1,801
Posted By BioGenomics
ChIPSeq results NEB kit and MiSeq run settings

Hi all,

Trying yet another protocol on our new MiSeq... We choose to go ahead with the NEB ChIPSeq lib prep kit (Ultra DNA in fact), but had some mixed library prep results:

--> After size...
Forum: Sample Prep / Library Generation 11-17-2014, 03:38 AM
Replies: 4
Views: 2,738
Posted By BioGenomics
Using v3 and running pool of 16s amplicon libs +...

Using v3 and running pool of 16s amplicon libs + Nextera XT small genome/large amplicon libs. So the 5 % PhiX might not be needed. Run still looking good (98% > Q30).
Forum: Sample Prep / Library Generation 11-16-2014, 08:44 PM
Replies: 4
Views: 2,738
Posted By BioGenomics
Hi NAH, Illumina TechSupp replied as such on the...

Hi NAH, Illumina TechSupp replied as such on the use of NextSeq500 protocol:

"All of Illumina platforms use isothermal amplification for clustering, and sequencing by synthesis for sequencing. So...
Forum: Sample Prep / Library Generation 11-13-2014, 04:04 PM
Replies: 4
Views: 2,738
Posted By BioGenomics
Question 16s updated NextSeq500 library prep for low concentration ok for MiSeq ?

Hi all, anybody has experience with using a 0.5 nM 16s library concentration (instead of 2nM) on the MiSeq ? The NextSeq500 has this protocol (updated October 2014, so more recent) and we thought to...
Forum: Sample Prep / Library Generation 11-12-2014, 11:12 PM
Replies: 19
Views: 7,054
Posted By BioGenomics
Hi nucacidhunter et al, anybody has experience...

Hi nucacidhunter et al, anybody has experience with using a 0.5 nM 16s library concentration (instead of 2nM) on the MiSeq ? The NextSeq500 has this protocol (updated October 2014, so more recent)...
Forum: Epigenetics 09-17-2014, 06:20 PM
Replies: 0
Views: 2,235
Posted By BioGenomics
ChIPSeq lilbrary prep for Miseq: NEB or TruSeq ?

Hi all,

is there a consensus on using NEB or Illumina TruSeq ChipSeq lib prep kits ? I assume the NEB is way cheaper anyway, but seemingly had better performance from the latest posts in 2013? I...
Forum: Illumina/Solexa 09-16-2014, 07:38 PM
Replies: 5
Views: 6,217
Posted By BioGenomics
NEB or Illumina ?

Hi all,

so is there a consensus on using NEB or Illumina ChipSeq lib prep kits ? I assume the NEB is way cheaper anyway, but seemingly had better performance from the latest post ?

thanks
...
Forum: Sample Prep / Library Generation 07-30-2014, 12:20 AM
Replies: 19
Views: 7,054
Posted By BioGenomics
I had another question concerning low cleaned...

I had another question concerning low cleaned amplicon concentration before indexing PCR. Can the Nextera indexing PCR cycle (8 cycles) be increased (to 10-12) without any issues to increase the...
Forum: Sample Prep / Library Generation 07-29-2014, 04:37 AM
Replies: 19
Views: 7,054
Posted By BioGenomics
Thanks for this nucacidhunter. So is 4 pM the...

Thanks for this nucacidhunter. So is 4 pM the optimal (clustering) conc for amplicon Seq ?

cheers
Forum: Sample Prep / Library Generation 07-28-2014, 11:59 PM
Replies: 19
Views: 7,054
Posted By BioGenomics
16s MiSeq Illumina library concentration and PhiX

Hi all,

I have 2 small questions concerning the 16s sequencing protocol for MiSEq:

1) Some samples have very low concentration so we are considering loading a 2pM library instead of the more...
Forum: Sample Prep / Library Generation 07-17-2014, 07:07 PM
Replies: 3
Views: 3,474
Posted By BioGenomics
Smile Thanks for this. Well some overlap would be nice...

Thanks for this. Well some overlap would be nice indeed, as this might improve assembly later on. I indeed read this trick, hope this also works as well with SeraMag beads (the ones I use). I also...
Forum: Sample Prep / Library Generation 07-17-2014, 04:42 PM
Replies: 3
Views: 3,474
Posted By BioGenomics
Question Nextera XT fragment size and MiSeq v3 read length clashing ?

Hi all,

I am planning a bacterial genome sequencing project (5 Mb) for around 80 samples to get good coverage. As the input material is limited, I need to use the Nextera XT kit (or standard...
Forum: Bioinformatics 12-08-2010, 06:41 PM
Replies: 0
Views: 3,325
Posted By BioGenomics
Post Rarefaction/saturation curve based on NGS data

Hi all,

most likely a simple question, but I'm looking for a tool (software, python/Perl/R script) that produces a rarefaction curve base on an input assembly (ACE would be easiest) to assess the...
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