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Forum: Academic/Non-Profit Jobs 05-17-2015, 01:12 PM
Replies: 0
Views: 1,442
Posted By jonathanjacobs
Exclamation Postdoctoral Research Associate Bioinformatics & Microbial Genomics

Postdoctoral Research Associate Bioinformatics & Microbial Genomics (http://www1.recruitingcenter.net/Clients/mriglobal/PublicJobs/controller.cfm?jbaction=JobProfile&Job_Id=11208&esid=az)
...
Forum: Academic/Non-Profit Jobs 12-16-2013, 03:09 PM
Replies: 1
Views: 5,422
Posted By jonathanjacobs
BUMPED. The position in my group is still...

BUMPED.

The position in my group is still open. Feel free to message me if you have any questions.
Forum: Sample Prep / Library Generation 12-02-2013, 09:22 AM
Replies: 0
Views: 1,649
Posted By jonathanjacobs
Question HELSR? Heterologus Elongation Ligation Reaction & Sequencing?

Anyone know what HELSR is for #ngs library prep?

Mentioned is this RFP from USMRIID:

https://www.fbo.gov/spg/USA/USAMRAA/DAMD17/W81XWH-14-R-0009/listing.html

My Google-Fu is failing me, and...
Forum: Ion Torrent 12-02-2013, 09:16 AM
Replies: 9
Views: 6,398
Posted By jonathanjacobs
CLC's assembler is quite good (and very fast) -...

CLC's assembler is quite good (and very fast) - so I would second that suggestion. Also, you may want to try IDBA's transcriptome assembler:...
Forum: Ion Torrent 11-25-2013, 09:29 AM
Replies: 2
Views: 3,350
Posted By jonathanjacobs
doing a second round of both 5' and 3' trimming...

doing a second round of both 5' and 3' trimming of P1 and A adapters (almost always) improves read mapping for Ion data (IME).
Forum: Ion Torrent 11-12-2013, 05:21 AM
Replies: 14
Views: 7,479
Posted By jonathanjacobs
We are using the RNAseq v2 kit routinely for...

We are using the RNAseq v2 kit routinely for viral RNA sequencing, miRNA sequencing, and polyA+ libraries too. Works quite well. We did have a Ashe of a bad lot / kit once and life tech replaced the...
Forum: Academic/Non-Profit Jobs 09-30-2013, 10:28 AM
Replies: 1
Views: 5,422
Posted By jonathanjacobs
Exclamation Postdoctoral Research Fellow Biosurveillance & Metagenomics

Postdoctoral Research Fellowship to Study Metagenomics of Indoor Air & Environmental Persistence of Antibiotic Resistance Markers


LINK TO APPLY: http://goo.gl/t66Klo

Founded in 1944,...
Forum: Ion Torrent 09-24-2013, 09:54 AM
Replies: 8
Views: 10,999
Posted By jonathanjacobs
Also - keep in mind that Q30 Ion data != Q30...

Also - keep in mind that Q30 Ion data != Q30 Illumina data since the base calling algorithms are different and the estimation/prediction of "quality" is inherently different between the base calling...
Forum: Ion Torrent 08-26-2013, 05:00 AM
Replies: 1
Views: 4,675
Posted By jonathanjacobs
You should post this to the Ion Community site...

You should post this to the Ion Community site with a copy of the logs from TMAP.
Forum: Ion Torrent 07-15-2013, 05:22 AM
Replies: 2
Views: 4,113
Posted By jonathanjacobs
Probably not. You'll get about 5M reads on a good...

Probably not. You'll get about 5M reads on a good day with the Ion318 - which is good enough for polyA+ transcriptome sequencing; comparable to what you might expect from an Affymetrix array. We also...
Forum: Ion Torrent 07-01-2013, 04:19 AM
Replies: 7
Views: 6,421
Posted By jonathanjacobs
For what it's worth - higher coverage will NOT...

For what it's worth - higher coverage will NOT not lead to better de novo assemblies. Once you hit about 40-50x , higher coverage may actually produce worse assemblies. Using an Ion318 for a 2MB...
Forum: Ion Torrent 05-13-2013, 05:26 PM
Replies: 2
Views: 5,206
Posted By jonathanjacobs
The PGM doesn't have a 10G chip. Do you...

The PGM doesn't have a 10G chip.

Do you mean the Proton system? That will get you about 100M reads at 200bp; should take a couple of hours on the hardware that ships with the Proton (if you use...
Forum: Ion Torrent 05-13-2013, 05:25 PM
Replies: 1
Views: 3,168
Posted By jonathanjacobs
For single read 200bp data - In our experience...

For single read 200bp data - In our experience with the PGM running 200bp reads - that's about right. You'll be lucky if you break 100K for your largest contig for most bacterial genomes with single...
Forum: Ion Torrent 05-13-2013, 05:21 PM
Replies: 3
Views: 3,308
Posted By jonathanjacobs
Should work fine - but you'll loose strandedness...

Should work fine - but you'll loose strandedness information if you have any overlapping ORFs on opposite strands.
Forum: Ion Torrent 02-07-2013, 04:51 AM
Replies: 9
Views: 3,666
Posted By jonathanjacobs
I doubt this would be a problem specific to the...

I doubt this would be a problem specific to the PGM.

If you are just looking at mature eukaryotic mRNAs, and have plenty of starting material, then using a two step process works very well 1)...
Forum: Bioinformatics 02-06-2013, 09:21 AM
Replies: 2
Views: 1,499
Posted By jonathanjacobs
Are you using GW6? Tracks is not the way to...

Are you using GW6?

Tracks is not the way to do this - you should use a Read Mapping file; not a Track file.

This might be a hack - but you might try annotating the genome with a custom...
Forum: Ion Torrent 08-14-2012, 12:38 PM
Replies: 4
Views: 3,151
Posted By jonathanjacobs
A couple suggestions that might help: First...

A couple suggestions that might help:

First - depending on your application, you may also want to look into a viral quasispecies analysis tool such as ShoRAH or QuRe - the viral quasispecies...
Forum: Ion Torrent 07-30-2012, 01:31 PM
Replies: 1
Views: 3,251
Posted By jonathanjacobs
We use CLCbio - and the current version (both 5.5...

We use CLCbio - and the current version (both 5.5 Beta and 5.1 Stable) has options for homopolymer filtering for SNP/Indel calling with 454 and Ion Torrent data. We haven't verified these indels by...
Forum: Bioinformatics 07-11-2012, 10:03 AM
Replies: 12
Views: 21,717
Posted By jonathanjacobs
Thumbs up Thank you - discovered Biopieces because of this...

Thank you - discovered Biopieces because of this post and, after some mucking around with macports and ruby installations on OSX, finally got it working. THANK YOU. Very handy set up tools.
Forum: Ion Torrent 07-09-2012, 07:59 AM
Replies: 27
Views: 18,988
Posted By jonathanjacobs
Smile @Ronan: We use GALAXY and CLCbio Genome Workbench...

@Ronan: We use GALAXY and CLCbio Genome Workbench in our shop and have a MiSeq and IonTorrent in house. we're mainly doing microbial and viral resequencing, but it seems as though de novo assembly...
Forum: Ion Torrent 04-09-2012, 04:03 AM
Replies: 18
Views: 10,377
Posted By jonathanjacobs
It actually an either/or question - not both. ...

It actually an either/or question - not both.

The idea behind using the BioAnalyzer is that you can assess your library's quality far far better than using a gel. When we first started running the...
Forum: Ion Torrent 03-21-2012, 06:43 AM
Replies: 15
Views: 14,689
Posted By jonathanjacobs
FWIW - there's a parrallel discussion about this...

FWIW - there's a parrallel discussion about this at the IonTorrent community here.

http://lifetech-it.hosted.jivesoftware.com/thread/2299?tstart=0

As Hmorrison mentioned - the 200nt kit...
Forum: Bioinformatics 02-28-2012, 10:01 AM
Replies: 8
Views: 10,967
Posted By jonathanjacobs
BUMPED. Thank you for this. We're using CLC...

BUMPED.

Thank you for this. We're using CLC Bio for routine analysis (which is really nice) but it doesn't support circular genome maps at the moment.

So far BRIG has done what I need. CIRCOS...
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