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Forum: De novo discovery 08-22-2013, 06:12 AM
Replies: 26
Views: 10,556
Posted By Cofactor Genomics
Well, your newly formed transcriptome assembly is...

Well, your newly formed transcriptome assembly is your reference, the raw read data used to generate the assembly is your data and you treat it like a RNA-seq project. In this manner, you align the...
Forum: De novo discovery 08-22-2013, 05:37 AM
Replies: 26
Views: 10,556
Posted By Cofactor Genomics
One metric you can look at to assess your...

One metric you can look at to assess your assembly is the percentage of reads that align back to your transcriptome assembly.
Forum: RNA Sequencing 08-20-2013, 02:33 PM
Replies: 6
Views: 1,341
Posted By Cofactor Genomics
Agreed with Bukowski and dpryan, What I have...

Agreed with Bukowski and dpryan,
What I have seen over a number of studies is that in order to characterize at the isoform level (and be confident) additional sequencing/coverage is necessary. This...
Forum: 454 Pyrosequencing 07-29-2013, 08:52 PM
Replies: 5
Views: 2,256
Posted By Cofactor Genomics
I am with chadn737 on that. You will not be...

I am with chadn737 on that.
You will not be sequencing very deep into the complexity of the pool on non-normalized 454 cDNA. However, maybe that is inherent in the design. You are likely not...
Forum: Core Facilities 07-29-2013, 08:43 PM
Replies: 16
Views: 8,106
Posted By Cofactor Genomics
Hi Vebaev, Our team takes in quite a few...

Hi Vebaev,
Our team takes in quite a few samples from Europe over the last 5 years.
Please contact me and happy to provide example projects and references. Our European projects are a great success...
Forum: General 07-29-2013, 08:37 PM
Replies: 1
Views: 17,104
Posted By Cofactor Genomics
Hi Monica, Did you ever have luck publishing...

Hi Monica,
Did you ever have luck publishing this story? I would be interested in the read and I am not finding it.

My best.
Jarret

Jarret Glasscock
Cofactor Genomics...
Forum: Service Providers 07-29-2013, 08:34 PM
Replies: 13
Views: 8,665
Posted By Cofactor Genomics
Hi Melissa, Our company's specialty is...

Hi Melissa,

Our company's specialty is RNAseq, with normalized cDNA being a component of that.
We also guarantee our output, quality, and turnaround time so you won't have to deal with the...
Forum: Illumina/Solexa 07-29-2013, 08:14 PM
Replies: 31
Views: 14,234
Posted By Cofactor Genomics
Patent information on it can be found at: ...

Patent information on it can be found at:

https://docs.google.com/viewer?url=patentimages.storage.googleapis.com/pdfs/US20130079231.pdf

It reminds me of human genome project clone sequencing at...
Forum: Bioinformatics 07-29-2013, 08:01 PM
Replies: 2
Views: 673
Posted By Cofactor Genomics
Hi ZoeG, I wonder what your ultimate goal is in...

Hi ZoeG,
I wonder what your ultimate goal is in the project.

My team uses these unmapped reads many times in a way to build confidence in a possible insertion sequence between the reference and...
Forum: Sample Prep / Library Generation 07-24-2013, 07:34 AM
Replies: 4
Views: 5,457
Posted By Cofactor Genomics
Have you run any qc on the data (FASTQC etc)? I...

Have you run any qc on the data (FASTQC etc)? I would be suspect of the data and not the BED file if you are seeing few reads map back to the regions. I do not believe there are different BED files...
Forum: Events / Conferences 06-03-2013, 08:03 AM
Replies: 2
Views: 1,131
Posted By Cofactor Genomics
Missed the talk? Watch the video here:...

Missed the talk? Watch the video here: http://bit.ly/18JjZGy
Forum: Events / Conferences 05-24-2013, 12:05 PM
Replies: 2
Views: 1,131
Posted By Cofactor Genomics
If you haven't already, be sure to sign up for...

If you haven't already, be sure to sign up for our webinar taking place next Friday at 12 CST: http://www.cofactorgenomics.com/blog/2013/de-novo-assembly-webinar-may-31st
Forum: Events / Conferences 05-03-2013, 12:59 PM
Replies: 2
Views: 1,131
Posted By Cofactor Genomics
Cofactor Genomics De Novo Assembly Webinar - May 31st

Cofactor Genomic's next webinar will focus on Cofactor's De Novo Assembly advances and take place on Friday, May 31st at 12:00 PM CST. From the beginning, our team has been developing and refining...
Forum: Metagenomics 04-30-2013, 10:34 AM
Replies: 5
Views: 1,365
Posted By Cofactor Genomics
Hello NewBioinfo, I agree with JackieBadger on...

Hello NewBioinfo,
I agree with JackieBadger on taking these steps to do all you can for the preservation of those RNA samples.

What becomes the real determinant is that assessment (QC) that you...
Forum: Bioinformatics 04-30-2013, 09:21 AM
Replies: 3
Views: 686
Posted By Cofactor Genomics
Hello Guigra, Can you share your alignment...

Hello Guigra,
Can you share your alignment parameters with the group here... as well as confirm you expect the two to align because you established this with the prior BWA alignments? There are a...
Forum: RNA Sequencing 04-30-2013, 09:11 AM
Replies: 8
Views: 8,498
Posted By Cofactor Genomics
Hello Obscurite, We typically see higher...

Hello Obscurite,

We typically see higher than 80% mapping rate for our RNA-Seq differential expression projects as well.

I agree with alexdobin. One of the next things to check is for...
Forum: General 04-25-2013, 08:35 AM
Replies: 23
Views: 113,026
Posted By Cofactor Genomics
Congrats! Jarret Glasscock Cofactor...

Congrats!

Jarret Glasscock
Cofactor Genomics
http://www.cofactorgenomics.com
Forum: Bioinformatics 04-25-2013, 07:28 AM
Replies: 6
Views: 1,818
Posted By Cofactor Genomics
Hi wilson90, Over the last 5 years our team has...

Hi wilson90,
Over the last 5 years our team has developed software we have used in Differential expression and splicing (Cofactor's Active Site). As of this year we offer the analysis as a service...
Forum: Illumina/Solexa 04-19-2013, 02:46 PM
Replies: 3
Views: 1,361
Posted By Cofactor Genomics
Hi, Although our team has not seen this many...

Hi,
Although our team has not seen this many transcripts under a given locus... what we have tended to do is set those loci with a given blastx hit as tier one transcripts (ie given them a higher...
Forum: Genomic Resequencing 04-19-2013, 02:15 PM
Replies: 2
Views: 1,449
Posted By Cofactor Genomics
What our team has found is that depending on...

What our team has found is that depending on whether you are working with a genome of 5Mb, 100Mb, or 3Gb... you will have very different approaches to the library, sequencing, assembly, and...
Forum: Service Providers 04-19-2013, 02:08 PM
Replies: 162
Views: 129,052
Posted By Cofactor Genomics
Hi Eric, Can you help us out by updating our...

Hi Eric,
Can you help us out by updating our list to:

Illumina/454/SOLiD/Ion/Informatics

Jarret Glasscock
Cofactor Genomics
http://www.cofactorgenomics.com
Forum: Illumina/Solexa 04-15-2013, 07:05 PM
Replies: 9
Views: 3,217
Posted By Cofactor Genomics
Have you stepped it through its paces yet? ie...

Have you stepped it through its paces yet?
ie compared it to other transcriptome assemblers in context of a RNA-seq set against well characterized gene models?
Will it only take ILMN reads, or will...
Forum: Illumina/Solexa 03-27-2013, 09:20 PM
Replies: 1
Views: 1,663
Posted By Cofactor Genomics
Were you expecting more similar N50s because the...

Were you expecting more similar N50s because the organisms were very similar?
Were the two projects sequenced to the same depth using the same library type and read configuration? How about the...
Forum: RNA Sequencing 03-27-2013, 09:10 PM
Replies: 12
Views: 3,222
Posted By Cofactor Genomics
We see similar things in many of our RNA-seq...

We see similar things in many of our RNA-seq projects. Agreeing with Jeremy, on it is very important to employ a filter for coverage to separate noise from signal. We see expressed regions with...
Forum: Events / Conferences 03-20-2013, 10:51 AM
Replies: 0
Views: 764
Posted By Cofactor Genomics
Cofactor Genomics RNA-seq Webinar

Cofactor Genomics will be holding a webinar on our RNA-seq process and pipeline on March 22nd at 12:00P.M. Central Time. Registration is free and open to the public.

During the webinar, you will...
Showing results 1 to 25 of 52

 


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