SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 129
Search took 0.01 seconds.
Search: Posts Made By: epistatic
Forum: Ion Torrent 06-08-2016, 04:32 AM
Replies: 37
Views: 38,695
Posted By epistatic
https://www.thermofisher.com/order/catalog/product...

https://www.thermofisher.com/order/catalog/product/F555S
Forum: Illumina/Solexa 01-11-2016, 09:26 AM
Replies: 17
Views: 3,641
Posted By epistatic
Deep sequence known regions known for targeted...

Deep sequence known regions known for targeted therapy for that cancer type. A handful of regions is all that is needed for lung. If they just want a signal of cancer before they do a larger panel,...
Forum: The Pipeline 01-11-2016, 09:18 AM
Replies: 16
Views: 17,679
Posted By epistatic
MiniSeq name now taken by Illumina. Original...

MiniSeq name now taken by Illumina. Original MiniSeq now the Qiagen GeneReader?


Introducing the MiniSeq™ System: Our simplest, most affordable sequencing solution yet.

Speakers:
Stephen...
Forum: Bioinformatics 09-02-2015, 04:32 AM
Replies: 5
Views: 2,457
Posted By epistatic
There were a few bugs in the software causing...

There were a few bugs in the software causing high counts and also duplication of columns during output concatenation that seem resolved when I contacted the developers. I only used the program a few...
Forum: Bioinformatics 12-09-2013, 01:26 PM
Replies: 1
Views: 947
Posted By epistatic
Try Btrim. You can create an index sequence txt...

Try Btrim. You can create an index sequence txt and trim 3' and/or 5'.

http://graphics.med.yale.edu/trim/readme
Forum: Sample Prep / Library Generation 09-30-2013, 03:47 PM
Replies: 1
Views: 2,027
Posted By epistatic
Epicentre's Ribo-zero magnetic kit and 100 ng of...

Epicentre's Ribo-zero magnetic kit and 100 ng of RNA = 0.2% ribosomal bases
Epicentre's Ribo-zero magnetic kit and 1 ug of RNA = 30% ribosomal bases
Forum: Illumina/Solexa 09-23-2013, 07:33 AM
Replies: 14
Views: 10,351
Posted By epistatic
Qiagen's GeneRead can be used to amplify either...

Qiagen's GeneRead can be used to amplify either all exons or the whole mitochondria in smaller amplicons. The two large amplicons yield more errors from the long PCR and can confound heteroplasmy...
Forum: Ion Torrent 09-20-2013, 06:59 AM
Replies: 5
Views: 4,316
Posted By epistatic
These are worthless. Recycle or get crafty and...

These are worthless. Recycle or get crafty and sell on etsy.
Forum: Illumina/Solexa 08-20-2013, 02:48 PM
Replies: 26
Views: 14,519
Posted By epistatic
"According to the company, the new kit will...

"According to the company, the new kit will enable new applications on the MiSeq such as exome sequencing and transcriptome sequencing."

With 80% of exons being <200 bp (ave 170 bp), does Illumina...
Forum: Illumina/Solexa 08-05-2013, 11:25 AM
Replies: 15
Views: 20,010
Posted By epistatic
no, see the description above regarding exon...

no, see the description above regarding exon size. Our exome libraries are usually 150-200 bp insert, run PE-76. Take the yield you get from MiSeq at the shorter PE, not PE-150 or PE-250. These...
Forum: Illumina/Solexa 08-05-2013, 11:20 AM
Replies: 55
Views: 28,524
Posted By epistatic
Did you run human genomic DNA as input? If so,...

Did you run human genomic DNA as input? If so, how much do you recommend as input? I took a look at Bioo's kit and they used 50 ng of bacterial DNA as input. Understand this for straight bacterial...
Forum: Bioinformatics 05-03-2013, 12:34 PM
Replies: 5
Views: 2,457
Posted By epistatic
I should have caught this, the output of EDGE-pro...

I should have caught this, the output of EDGE-pro is not logical with the read count per sample. SUM of counts from one sample column = 6,705,152,768!
Forum: Bioinformatics 05-03-2013, 12:17 PM
Replies: 5
Views: 2,457
Posted By epistatic
Thank you very much for your reply and help. ...

Thank you very much for your reply and help.

http://ccb.jhu.edu/software/EDGE-pro/
T. Magoc, D. Wood, and S.L. Salzberg. EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes....
Forum: Bioinformatics 05-03-2013, 08:28 AM
Replies: 5
Views: 2,457
Posted By epistatic
EDGE-pro into DESeq, DESeq run error?

Hi All,

I am doing rRNA reduced, strand specific RNA-seq in bacterial species and decided to try EDGE-pro (Estimated Degree of Gene Expression in Prokaryotic Genomes) and then run the count table...
Forum: Illumina/Solexa 03-29-2013, 01:28 PM
Replies: 8
Views: 4,173
Posted By epistatic
Apologies for the unclear terminology. I should...

Apologies for the unclear terminology. I should have said I made the amplicon larger. If I just used the standard amplicon nextera would integrate often only once or if twice it would cut off parts...
Forum: Illumina/Solexa 03-28-2013, 07:38 PM
Replies: 8
Views: 4,173
Posted By epistatic
How well did the tagmentation work with FFPE...

How well did the tagmentation work with FFPE samples? You may have many fragments with one integration site, not allowing for the majority of your sample to have both adapters for the PCR step.
...
Forum: Ion Torrent 03-04-2013, 04:35 AM
Replies: 37
Views: 38,695
Posted By epistatic
It would be cheaper and easier to add a universal...

It would be cheaper and easier to add a universal sequence and then do a short second PCR adding on the adapters (and indexing) using home made oligos or Illumina's Indexing kit. Same way TruSeq...
Forum: Ion Torrent 03-02-2013, 11:07 AM
Replies: 37
Views: 38,695
Posted By epistatic
Me too, I was hoping to be able to do the...

Me too, I was hoping to be able to do the Ampliseq reaction, treat with USER to remove the dUTP bases and then do the standard blunt end ligation prep putting on Illumina adapters. Ampliseq looks...
Forum: Illumina/Solexa 03-02-2013, 11:03 AM
Replies: 3
Views: 2,770
Posted By epistatic
We have been struggling with the Nextera exome...

We have been struggling with the Nextera exome prep. We definitely input 50 ng of DNA (picogreen and Qubit) as directed and all of our samples came out to a 2 kb mean fragment size. It was...
Forum: Core Facilities 10-31-2012, 11:54 AM
Replies: 18
Views: 10,100
Posted By epistatic
I have strong interest in a Proton but would not...

I have strong interest in a Proton but would not buy one yet.
A) Site in my state bought one, it arrived and is sitting in a box until it can be installed in December. What are install specs?
B) I...
Forum: Illumina/Solexa 10-14-2012, 11:30 AM
Replies: 2
Views: 2,734
Posted By epistatic
Currently runs cannot be requeued for analysis, I...

Currently runs cannot be requeued for analysis, I have to rerun analysis using MiSeq reporter locally. You can also ask nicely and see if a dev will alter sample sheet for your chosen application...
Forum: Illumina/Solexa 10-10-2012, 06:47 AM
Replies: 2
Views: 2,925
Posted By epistatic
I am glad I was skeptical when I was told our...

I am glad I was skeptical when I was told our HiSeq 2500 upgrade would allow >= 80% Q30 on PE-150 runs in the fast run mode and to expect >= 95% Q30 for PE-100. I was hoping to run TSCAP 250 bp...
Forum: Illumina/Solexa 10-10-2012, 06:42 AM
Replies: 2
Views: 987
Posted By epistatic
February for us... originally told Oct/Nov 2012.

February for us... originally told Oct/Nov 2012.
Forum: Ion Torrent 10-09-2012, 02:07 PM
Replies: 70
Views: 18,348
Posted By epistatic
PGM can handle low diversity runs, something the...

PGM can handle low diversity runs, something the MiSeq struggles with. Amplicon runs or samples for RNA-editing would be good to reason to have a PGM around.
Forum: Illumina/Solexa 10-09-2012, 02:04 PM
Replies: 2
Views: 2,925
Posted By epistatic
HiSeq 2500 run, not hopeful on a quality PE-150 quick run

The data set from the quick run mode on the HS2500 posted isn't too hopeful to have the proposed MiSeq run quality with a shorter run. Is it still spec'd to run PE-150 at a decent % >Q30?
...
Showing results 1 to 25 of 129

 


All times are GMT -8. The time now is 04:46 PM.


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