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Forum: Academic/Non-Profit Jobs 01-02-2017, 04:23 PM
Replies: 1
Views: 4,279
Posted By sci_guy
Updated details

The advertisement is on the CSIRO Vacancies Hub (https://jobs.csiro.au/job/Various-Postdoctoral-Fellowship-Future-Science-Platforms-Probing-Biosystems-%285%29/381836700/).

I've updated the...
Forum: Academic/Non-Profit Jobs 12-23-2016, 08:12 PM
Replies: 1
Views: 4,279
Posted By sci_guy
Postdoctoral Fellow (Epigenetics Liquid Biopsy Markers) - CSIRO, Sydney, Australia

Postdoctoral Fellowship on a project seeking to find and characterise circulating cell-free DNA biomarkers of traumatic brain injury.


Based at CSIRO, Sydney, NSW, Australia
AU $78k to $88k...
Forum: Academic/Non-Profit Jobs 10-12-2012, 08:24 PM
Replies: 0
Views: 4,230
Posted By sci_guy
Postdoc/Research Engineer - Systems Biology/Software Dev - CSIRO, Sydney, Australia

Position open until 11:30 pm AEST on 21 October 2012.

Role Overview

CSIRO Animal, Food and Health Sciences are looking for an enthusiastic Postdoctoral Fellow or research engineer who will work...
Forum: Illumina/Solexa 06-27-2011, 02:31 AM
Replies: 145
Views: 333,161
Posted By sci_guy
Could be leftover activity. But I would assume...

Could be leftover activity. But I would assume that the chaotropic salts and EtOH in the column would kill the activity.

Some degradation of the 3' end in the Y-tail is not a problem. The PCR...
Forum: Introductions 06-27-2011, 01:32 AM
Replies: 373
Views: 179,479
Posted By sci_guy
Hi Aeonsim, Wes Barris and Brian Dalrymple...

Hi Aeonsim,

Wes Barris and Brian Dalrymple at the CSIRO are experts in this field. Brian maybe sympathetic as he is a Kiwi (as am I) ;)

http://www.csiro.au/people/Brian.Dalrymple.html...
Forum: Introductions 06-27-2011, 01:19 AM
Replies: 373
Views: 179,479
Posted By sci_guy
Hello from Sci_guy

Hi,

My name is Jason and I work in Sydney for the CSIRO. I was a molecular biologist but now I've gone to the dark side and exchanged my pipettes for a Linux shell. I've been involved with mostly...
Forum: Illumina/Solexa 06-27-2011, 01:11 AM
Replies: 145
Views: 333,161
Posted By sci_guy
Hi nbogard, Exonucleases in the ligase prep...

Hi nbogard,

Exonucleases in the ligase prep can chew off the adaptor "A" overhang. Two of these blunt-end ligated together will amplify nicely. While the probability of exonuclease activity and...
Forum: Sample Prep / Library Generation 03-15-2011, 09:48 PM
Replies: 19
Views: 7,756
Posted By sci_guy
Hi Berthold, At least three ways to do it. ...

Hi Berthold,

At least three ways to do it.
1) Write a Perl script to remove exact matches. Parse the FASTQ, and look for the primer in each read with regular expressions. Trim the reads with hits...
Forum: General 11-03-2010, 02:04 AM
Replies: 2
Views: 4,184
Posted By sci_guy
Hi Simone, I use MspI quite a bit, 200 - 300...

Hi Simone,

I use MspI quite a bit, 200 - 300 U sounds excessive. Try Phenol/Chloroform/Isoamyl alcohol treating your DNA to make sure it is clean. You could also try a commercial (or some plasmid)...
Forum: General 11-03-2010, 01:59 AM
Replies: 11
Views: 4,953
Posted By sci_guy
SHRiMP is very robust to INDELs, but is very slow...

SHRiMP is very robust to INDELs, but is very slow (as it performs Smith-Waterman alignments).
Forum: Epigenetics 11-03-2010, 01:36 AM
Replies: 13
Views: 10,522
Posted By sci_guy
Can you be more specific? What is your budget,...

Can you be more specific? What is your budget, what is the organism, are you doing comparisons? Are you doing whole genome BS-seq or some form of complexity reduction, such as reduced representation...
Forum: Bioinformatics 07-22-2010, 08:30 PM
Replies: 24
Views: 5,309
Posted By sci_guy
I also also another unfortunate soul dealing with...

I also also another unfortunate soul dealing with SOLiD bisulfite reads. I also know that Thomas Preiss' group in Sydney is working on RNA methylation using SOLiD.
Forum: Bioinformatics 07-22-2010, 08:21 PM
Replies: 40
Views: 65,555
Posted By sci_guy
Not that I've heard of.

Not that I've heard of.
Forum: Illumina/Solexa 05-05-2010, 03:53 PM
Replies: 145
Views: 333,161
Posted By sci_guy
@kr067: No. Read the pdf posted by clpX above.

@kr067: No. Read the pdf posted by clpX above.
Forum: Bioinformatics 03-25-2010, 03:41 PM
Replies: 40
Views: 65,555
Posted By sci_guy
Cool. Thanks for that. There's nothing like...

Cool. Thanks for that.

There's nothing like empirical data to disprove an hypothesis ;)
Forum: Bioinformatics 03-22-2010, 03:14 PM
Replies: 40
Views: 65,555
Posted By sci_guy
I'm reading the GSNAP paper more throughly now as...

I'm reading the GSNAP paper more throughly now as it looks really good for a project I'm involved with - variant detection in a region of linkage.

The last sentence of the introduction is: "The...
Forum: Bioinformatics 03-22-2010, 02:59 PM
Replies: 40
Views: 65,555
Posted By sci_guy
Hua used an interesting recursive strategy to map...

Hua used an interesting recursive strategy to map more maps back to the Arabidopsis genome. After aligning she took the unmapped reads and chopping off the first base and the last few bases, then...
Forum: Bioinformatics 03-16-2010, 01:57 AM
Replies: 52
Views: 43,885
Posted By sci_guy
I am a molecular biologist/biochemist but I can...

I am a molecular biologist/biochemist but I can also do bioinformatics and biostatistics (lite). I imagine your professor is of a biological background and doesn't fully appreciate the statistics....
Forum: Bioinformatics 03-15-2010, 07:17 PM
Replies: 40
Views: 65,555
Posted By sci_guy
@lh3. I'm going to workshop over the next couple...

@lh3. I'm going to workshop over the next couple of days. It seems somebody else in my organisation has been using BSMAP with Arabidopsis bisulphite-Seq data. Below is their talk abstract. BSMAP...
Forum: Bioinformatics 03-15-2010, 05:47 PM
Replies: 40
Views: 65,555
Posted By sci_guy
Thanks for the heads-up on GSNAP. I just had a...

Thanks for the heads-up on GSNAP. I just had a look at the paper. It looks very nice. Particularly if they release a colorspace version, I am stuck with SOLiD colorspace data at present :confused: I...
Forum: Bioinformatics 03-15-2010, 02:24 PM
Replies: 40
Views: 65,555
Posted By sci_guy
I don't have access to the slides but the...

I don't have access to the slides but the material is covered essentially in their BSMAP (http://seqanswers.com/forums/showthread.php?p=15437#post15437) paper.

lh3 - Yes, I forgot about Novoalign....
Forum: Bioinformatics 03-12-2010, 08:51 PM
Replies: 8
Views: 3,962
Posted By sci_guy
I agree with drio. It's a old classical computer...

I agree with drio. It's a old classical computer science problem. Google "Intersection of sorted lists". If your lists aren't sorted then use GNU sort beforehand. You only need to write a shell...
Forum: Bioinformatics 03-12-2010, 08:30 PM
Replies: 40
Views: 65,555
Posted By sci_guy
I saw Wei Li talk about BSMAP at the AACR 2010...

I saw Wei Li talk about BSMAP at the AACR 2010 Cancer Epigenetics meeting. It was a nice talk. I like their use of what cytosines are present in the read to extract as much information as possible...
Forum: Bioinformatics 03-12-2010, 08:25 PM
Replies: 40
Views: 65,555
Posted By sci_guy
Thanks! I'll take a look. I have more SOLiD data...

Thanks! I'll take a look. I have more SOLiD data coming my way soon.
Forum: Bioinformatics 11-10-2009, 01:49 PM
Replies: 10
Views: 5,295
Posted By sci_guy
@Nils; I am amused :D The SAM munging Perl...

@Nils; I am amused :D The SAM munging Perl script in the 1.3.0 SHRiMP distribution is actually one authored by you.
Showing results 1 to 25 of 83
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