SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 22 of 22
Search took 0.00 seconds.
Search: Posts Made By: HeidiJTP
Forum: Academic/Non-Profit Jobs 05-05-2016, 08:15 AM
Replies: 0
Views: 2,648
Posted By HeidiJTP
Research Technician @ Harbor Branch, Florida Atl Univ

Senior Research Technician Needed

**We have a QuantStudio and are getting a MinION**

For more information about us: http://pbbegenetics.wix.com/pbbe

Or contact: hpagan1@fau.edu


Job...
Forum: Academic/Non-Profit Jobs 05-06-2015, 06:37 AM
Replies: 0
Views: 1,579
Posted By HeidiJTP
PostDoc - Immunogenetics: Harbor Branch Oceanographic Institute @ FAU

Harbor Branch Oceanographic Institute at Florida Atlantic university (HBOI-FAU) seeks candidates for a postdoctoral position in the immunogenetics of marine mammals based at the HBOI site in Ft....
Forum: Academic/Non-Profit Jobs 03-30-2015, 12:00 PM
Replies: 0
Views: 1,474
Posted By HeidiJTP
Bioinformatics Research Faculty Position: Florida Atlantic University

Harbor Branch Oceanographic Institute, located in Fort Pierce Florida, seeks candidates for an Assistant, Associate, or Full Research Professor with expertise in Bioinformatics. Applications are...
Forum: Genomic Resequencing 09-24-2014, 11:12 AM
Replies: 1
Views: 1,725
Posted By HeidiJTP
Variant found in priming site

I sequenced barcoded PCR amplicons on Ion Torrent PGM, and a subset of samples were also Sanger sequenced to confirm variable sites.

I first noticed that a variant was showing up in the forward...
Forum: Bioinformatics 03-03-2014, 08:02 AM
Replies: 3
Views: 1,690
Posted By HeidiJTP
Sridhar, Were you ever able to resolve this...

Sridhar,

Were you ever able to resolve this problem? I am having the same issue.
Forum: Bioinformatics 02-02-2014, 05:51 PM
Replies: 0
Views: 1,322
Posted By HeidiJTP
Phase genotypes in Galaxy

I used Galaxy to generate vcf files, but the output has unphased genotypes. Are there any options for obtaining the phased genotypes through Galaxy?

My data were generated from 350 bp amplicons...
Forum: Ion Torrent 01-12-2014, 06:00 AM
Replies: 5
Views: 4,995
Posted By HeidiJTP
Thanks GenoMax! And I appreciate that you...

Thanks GenoMax! And I appreciate that you included the documentation from Ion Torrent.
Forum: Ion Torrent 01-11-2014, 08:10 PM
Replies: 5
Views: 4,995
Posted By HeidiJTP
Thanks for the help! I changed it to...

Thanks for the help! I changed it to "fastqsanger" under Datatype as suggested, and this seems to have done the trick so that I don't need to rerun FASTQ Groomer.

Can anyone verify that Sanger is...
Forum: Ion Torrent 01-11-2014, 07:51 AM
Replies: 5
Views: 4,995
Posted By HeidiJTP
Ion Torrent FastQ Analysis on Galaxy

I have two questions about analyzing PGM FastQ files using Galaxy.

1) Can someone confirm if Ion Torrent FastQ files are in Sanger format?

I believe they are based on information from the wiki...
Forum: Ion Torrent 06-14-2013, 07:23 AM
Replies: 9
Views: 6,662
Posted By HeidiJTP
Thank you everyone for your suggestions, and for...

Thank you everyone for your suggestions, and for the tip that everything's available on github. I watched a webinar yesterday for the Ion Reporter Software, in which the instructor stated that only...
Forum: Ion Torrent 06-12-2013, 09:26 AM
Replies: 9
Views: 6,662
Posted By HeidiJTP
Options for PGM Variant Analysis

I am preparing to order barcoded primers for a sequencing project on the PGM, and would appreciate some feedback on the options for data analysis before I make this purchase. We are sequencing 4 loci...
Forum: Ion Torrent 03-27-2013, 06:51 AM
Replies: 10
Views: 11,673
Posted By HeidiJTP
genseq - thanks for the latest info! How...

genseq - thanks for the latest info!

How about the NEXTflex kits? Anyone had experience with their DNA-Seq kits or the barcoding?...
Forum: Pacific Biosciences 02-23-2013, 10:51 AM
Replies: 12
Views: 5,220
Posted By HeidiJTP
Thanks again for the information rhall, I...

Thanks again for the information rhall, I appreciate it. By the way, this was for a 2kb library.
Forum: Pacific Biosciences 02-18-2013, 09:45 AM
Replies: 12
Views: 5,220
Posted By HeidiJTP
Thanks for the feedback rhall. I think the...

Thanks for the feedback rhall.

I think the post-filter read # aligns pretty well with 38.6% productivity 1 (~75k pre-filter reads, ~29k post-filter). Readlength mean is 3,701 bp and quality is...
Forum: Pacific Biosciences 02-14-2013, 08:12 AM
Replies: 12
Views: 5,220
Posted By HeidiJTP
PacBio ZMW Loading Productivity 2

I recently got back my first data set from a PacBio run and was wondering what are 'typical' values for the different productivity levels? Here's what I received:

4.8% ZMW Loading for Productivity...
Forum: Sample Prep / Library Generation 06-14-2012, 06:13 AM
Replies: 2
Views: 2,452
Posted By HeidiJTP
Thanks krobison, I appreciate the suggestion and...

Thanks krobison, I appreciate the suggestion and will look into this paper and similar methods for ideas. By the way, I have also found your blog very useful for staying up-to-date on the latest...
Forum: Sample Prep / Library Generation 06-12-2012, 07:11 AM
Replies: 2
Views: 2,452
Posted By HeidiJTP
Circularization of Large Target Fragments

Hi all,

I would like to target a ~10 kb region for NGS. I was looking at a paper by Myllykangas et al. (http://www.biomedcentral.com/1472-6750/11/122/) which circularizes a target region and...
Forum: General 05-14-2012, 11:45 AM
Replies: 6
Views: 2,755
Posted By HeidiJTP
MinION does sound amazing, but I don't think I...

MinION does sound amazing, but I don't think I can wait that patiently :)

What about the methods described by Lindsay, Bonfield, and Hurles (2005) "Shotgun haplotyping: a novel method for...
Forum: General 05-14-2012, 05:59 AM
Replies: 6
Views: 2,755
Posted By HeidiJTP
I realize this is an older thread, but I have a...

I realize this is an older thread, but I have a similar situation and was wondering which approach you used. I want to genotype a full gene and include 5' regulatory sequence as well for...
Forum: Bioinformatics 01-24-2012, 06:02 AM
Replies: 20
Views: 18,330
Posted By HeidiJTP
I think there are two problems here: 1)...

I think there are two problems here:

1) Display of NNNNs instead of sequence
This seems to be related in part to the actual terminal window. I thought it was weird that the NNNs don't appear...
Forum: Bioinformatics 01-24-2012, 04:55 AM
Replies: 20
Views: 18,330
Posted By HeidiJTP
Thanks for the suggestion Tally, I just reran...

Thanks for the suggestion Tally, I just reran everything and used the command view instead of import, but still no luck
Forum: Bioinformatics 01-23-2012, 06:05 AM
Replies: 20
Views: 18,330
Posted By HeidiJTP
I am also having this problem, where the first 80...

I am also having this problem, where the first 80 bases are present, then mostly Ns except in a few positions where aligned reads appear. I am just running a test set to try to learn the process, so...
Showing results 1 to 22 of 22

 


All times are GMT -8. The time now is 08:37 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO