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Forum: Core Facilities 11-13-2013, 06:54 AM
Replies: 9
Views: 6,597
Posted By genbio64
With all of the academic core facilities and...

With all of the academic core facilities and expertise available why would anyone waste time with an outside company like Otogenetics?
Forum: Core Facilities 09-18-2013, 06:52 AM
Replies: 11
Views: 3,158
Posted By genbio64
NewBioinfo, Our facility does offer that and...

NewBioinfo,
Our facility does offer that and we are stateside. I sent you a PM.
Forum: Illumina/Solexa 02-18-2013, 09:09 AM
Replies: 32
Views: 16,754
Posted By genbio64
Phillip, Could you post a quick diagram of...

Phillip,
Could you post a quick diagram of that indexing method please?
Forum: Illumina/Solexa 01-28-2013, 11:05 AM
Replies: 7
Views: 2,242
Posted By genbio64
Is this feature new in the last software update?...

Is this feature new in the last software update? Illumina had told us there was virtually no flexibility when it came to the downstream pipelines through MSR.
Forum: Illumina/Solexa 01-18-2013, 09:52 AM
Replies: 31
Views: 14,237
Posted By genbio64
from what I have been told its kind of a hybrid...

from what I have been told its kind of a hybrid optical mapping/mate pair strategy where they cut the reads up at specific points, add specific primer pairs across the length, sequence and then...
Forum: Illumina/Solexa 01-08-2013, 09:25 AM
Replies: 1
Views: 1,347
Posted By genbio64
MiSeq for library QC

With the announcement of the new micro and nano kits, is it better to use one of these with more cycles vs running the 2x26-bp for library validation? Granted the cost will be lower, and slightly...
Forum: General 09-14-2012, 07:51 AM
Replies: 7
Views: 2,589
Posted By genbio64
James, I sent you an email but we are using...

James,
I sent you an email but we are using that LIMS.
Forum: Service Providers 09-14-2012, 07:45 AM
Replies: 9
Views: 5,952
Posted By genbio64
The costs of sequencing will vary depending on...

The costs of sequencing will vary depending on where you go. A WGS at 30x will typically cost you >$6k and a few RNA-seq samples can be done in 1 lane of a HiSeq. Exomes and targeted seq samples can...
Forum: Core Facilities 08-21-2012, 09:26 AM
Replies: 11
Views: 5,921
Posted By genbio64
@pmiguel, is that standard Illumina supported...

@pmiguel, is that standard Illumina supported protocol to run 2 dark cycles?
Forum: Illumina/Solexa 07-24-2012, 01:31 PM
Replies: 10
Views: 5,632
Posted By genbio64
Dear Audio, No Illumiuna does not offer...

Dear Audio,
No Illumiuna does not offer methylated adapters to my knowledge as we have to custom order them.
Forum: Sample Prep / Library Generation 07-23-2012, 08:09 AM
Replies: 6
Views: 2,000
Posted By genbio64
Thanks but I was referring to sequencing...

Thanks but I was referring to sequencing performance? For example, sample coverage, anymore or less 5' or 3' bias, coverage of exons vs introns, coding vs non-coding genes?
Forum: Illumina/Solexa 07-20-2012, 11:05 AM
Replies: 10
Views: 3,417
Posted By genbio64
@jlove, did you figure out the SPRI works problem?

@jlove, did you figure out the SPRI works problem?
Forum: Sample Prep / Library Generation 07-20-2012, 11:02 AM
Replies: 6
Views: 2,000
Posted By genbio64
TruSeq vs Nexterra

I was wondering if anyone had an empirical evidence in the comparison between the TruSeq and Nexterra protocols? We have been considering switching over to the Epicentre products exclusively but lack...
Forum: Core Facilities 07-18-2012, 12:31 PM
Replies: 0
Views: 1,297
Posted By genbio64
default RNA-Seq library prep

What with all the developments in the RNA-Seq library prep field our lab is contemplating moving away from the Illumina Tru-Seq RNA kits and using the Script-Seq kits instead. Between the two the...
Forum: Service Providers 07-11-2012, 12:48 PM
Replies: 2
Views: 2,163
Posted By genbio64
We can handle that project for you. Send me a PM...

We can handle that project for you. Send me a PM and I can arrange the details if you like.
Forum: Core Facilities 04-25-2012, 12:45 PM
Replies: 1
Views: 2,561
Posted By genbio64
Automated library prep

Greetings all,
It seems there are multiple options available for automating library preps for NGS. Our lab is currently evaluating several but the Integenex Apollo seems to have the lead since...
Forum: Core Facilities 04-05-2012, 07:05 PM
Replies: 11
Views: 8,851
Posted By genbio64
Ken Beckman at the University of Minnesota runs a...

Ken Beckman at the University of Minnesota runs a CLIA certified Core
Forum: Core Facilities 03-08-2012, 12:28 PM
Replies: 1
Views: 2,260
Posted By genbio64
Certified Service Provider (CSP): Is it worth it?

As the title implies I was wondering if attaining a Certified Service Provider status is worth the cost? I know Illumina charges $10k for the first platform and then $5k for each additional one...
Forum: Core Facilities 01-19-2012, 01:25 PM
Replies: 8
Views: 4,544
Posted By genbio64
Ion Torrent and desktop sequencing: The Death of the Core

Greetings everyone,
With all of the new exciting announcements involving the announcement of $1,000 genomes I assume people will scrutinize the NGS field closely. With both Illumina and Ion...
Forum: Bioinformatics 04-14-2011, 01:01 PM
Replies: 15
Views: 13,386
Posted By genbio64
@RockChalkJayhawk or ChrisL, Can one of you...

@RockChalkJayhawk or ChrisL,
Can one of you elaborate on that workflow?
Forum: Bioinformatics 03-22-2010, 11:05 AM
Replies: 6
Views: 2,266
Posted By genbio64
Comparison of alignment tools

Dear Seqanswers,
Recently my lab purchased a license for CLC genome workbench to use for our next-gen sequencing needs. We have been using Bowtie/SAM Tools but everyone else liked the ease of use...
Forum: Bioinformatics 03-19-2010, 11:08 AM
Replies: 10
Views: 13,034
Posted By genbio64
@nilshomer I'll try that. thanks

@nilshomer
I'll try that.

thanks
Forum: Bioinformatics 03-19-2010, 10:46 AM
Replies: 3
Igv
Views: 2,847
Posted By genbio64
@Thomas Doktor, Thanks for the info but...

@Thomas Doktor,
Thanks for the info but everytime I attempt to run the igvtools count command it tells me it cannot find the genome file, regardless if I give it the name "hg19" or the full path....
Forum: Bioinformatics 03-19-2010, 09:35 AM
Replies: 3
Igv
Views: 2,847
Posted By genbio64
Igv

Greetings All,
I have been using IGV to view my bowtie alignments in BAM format but am experiencing some difficulty. I have to drill down to the last 2 levels of sequence magnification to...
Forum: Bioinformatics 03-19-2010, 07:54 AM
Replies: 10
Views: 13,034
Posted By genbio64
Does anyone know of a way to use Samtools to...

Does anyone know of a way to use Samtools to split off individual chromosomes for easier viewing? If I attempt to use samtools view <myfile.bam> chr1 I receive a bam file that I can no longer view...
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