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Forum: Academic/Non-Profit Jobs 02-21-2017, 07:12 PM
Replies: 0
Views: 677
Posted By ohofmann
Staff positions at Genomics Platform Team, Melbourne

As part of the newly established Center for Cancer Research we have five openings for 3 year staff positions in bioinformatics, software engineering and research computing.

You can find...
Forum: Academic/Non-Profit Jobs 07-10-2013, 11:54 AM
Replies: 0
Views: 953
Posted By ohofmann
Post Junior and Senior Bioinformatician

We currently have openings at HSPH (http://compbio.sph.harvard.edu/chb/articles/come-work-with-us) for one senior...
Forum: Academic/Non-Profit Jobs 03-13-2012, 05:40 PM
Replies: 0
Views: 1,968
Posted By ohofmann
Computational biologist, Harvard School of Public Health

The HSPH Center for Health Bioinformatics (http://compbio.sph.harvard.edu/chb/) (CHB) is a center for bioinformatic research, services and training at the Harvard School of Public Health...
Forum: Bioinformatics 11-29-2011, 07:46 PM
Replies: 9
Views: 2,742
Posted By ohofmann
NovoAlign also handles IUPAC reference sequences....

NovoAlign also handles IUPAC reference sequences. There is a difference in how these are being handled -- Mosaik considers any base aligned to an IUPAC position a partial mismatch, NovoAlign does not...
Forum: Events / Conferences 09-24-2011, 12:52 PM
Replies: 1
Views: 2,475
Posted By ohofmann
Some talk coverage at...

Some talk coverage at http://fiamh.tumblr.com/post/10403157122/answering-the-demands-of-digital-genomics (and newer posts).
Forum: Bioinformatics 02-08-2011, 09:20 AM
Replies: 0
Views: 1,749
Posted By ohofmann
Reference-guided cDNA assembly using related genomes

Dear all,


taken a look through the forum to find related questions. While there are plenty of tools for reference guided RNA-seq assembly (TopHat/Cufflinks, etc.) in general is there anything...
Forum: Bioinformatics 11-17-2010, 03:02 AM
Replies: 27
Views: 10,393
Posted By ohofmann
Nils, congratulations on getting the publication...

Nils, congratulations on getting the publication out!

I'm about to give this a try on an odd data set -- 2kb of genomic sequence at an average (but far from uniform) coverage of around 100.000 X....
Forum: Bioinformatics 06-27-2010, 09:43 AM
Replies: 14
Views: 2,717
Posted By ohofmann
I'd rather keep it in a single section for now....

I'd rather keep it in a single section for now. Easy to zip through.. sometimes more informative subject lines would be nice, but the volume isn't so bad (yet) that a split is required.
Forum: Bioinformatics 05-15-2010, 10:42 AM
Replies: 27
Views: 10,393
Posted By ohofmann
Thanks for the swift reply ;-) Going to give it a...

Thanks for the swift reply ;-) Going to give it a try, we've got a nice test set to measure improvements right away. Will report back once I had a chance to tinker.
Forum: Bioinformatics 05-15-2010, 04:20 AM
Replies: 27
Views: 10,393
Posted By ohofmann
Nils, how much flexibility do I have with...

Nils, how much flexibility do I have with MINIMUM_ALLELE_PROBABILITY? Itching to give this a try with some high-coverage pathogen re-sequencing data, but we are particularly interested in rare...
Forum: Bioinformatics 04-26-2010, 07:45 PM
Replies: 366
Views: 198,340
Posted By ohofmann
Your cluster setup is blocking X11 / the...

Your cluster setup is blocking X11 / the graphical interface (or you are not exporting the display to your local machine if it does).
Forum: Bioinformatics 04-15-2010, 09:05 AM
Replies: 36
Views: 24,035
Posted By ohofmann
Problem with Helicos is that it doesn't come as...

Problem with Helicos is that it doesn't come as FASTQ (quality scores are assigned to reads, not nucleotides within the reads). The best (only?) way to handle this is to convert the original format...
Forum: Bioinformatics 03-16-2010, 02:04 PM
Replies: 34
Views: 9,875
Posted By ohofmann
What can I say, after ten years of cobbling...

What can I say, after ten years of cobbling together parsers I'm not asking for much anymore ;)
Forum: Bioinformatics 03-15-2010, 12:21 PM
Replies: 34
Views: 9,875
Posted By ohofmann
This looks terrific. Add in BEDTools and a few...

This looks terrific. Add in BEDTools and a few basic shell scripts and quite a lot additional glue can be dropped from workflows.
Forum: Events / Conferences 02-27-2010, 05:22 PM
Replies: 6
Views: 12,776
Posted By ohofmann
Notes from day 3...

Notes from day 3 (http://www.fiamh.info/articles/23/agbt-day-3) are up. Not sure whether to be excited or just plain scared...
Forum: Events / Conferences 02-26-2010, 06:30 PM
Replies: 6
Views: 12,776
Posted By ohofmann
Been cut'n'pasting Twitter notes, RSS feeds and...

Been cut'n'pasting Twitter notes, RSS feeds and FF comments at http://www.fiamh.info/category/agbt-2010/. Certainly not complete, but maybe an easy way to catch up if you do not have the time to...
Forum: Bioinformatics 02-19-2010, 06:58 AM
Replies: 4
Views: 3,482
Posted By ohofmann
Getting the same error using the `-c` flag; maybe...

Getting the same error using the `-c` flag; maybe indicative of something being wrong with my SRF files rather than the conversion process. I'll see if I can get this to work on public Helicos data...
Forum: Bioinformatics 02-18-2010, 05:34 PM
Replies: 4
Views: 3,482
Posted By ohofmann
Sorry, should have clarified that -- Helisphere...

Sorry, should have clarified that -- Helisphere even provides scripts that insert dummy quality values, but since we are trying to get a better handle on error profiles that is of course less than...
Forum: Bioinformatics 02-18-2010, 03:08 PM
Replies: 4
Views: 3,482
Posted By ohofmann
Helicos SRF to FASTQ

Dear all,



been trying to explore a number of Helicos runs. I have access to the read data both in Helicos' SMS format as well as their implementation of SRF (which does not bode well). Using...
Forum: Bioinformatics 10-17-2009, 08:45 AM
Replies: 6
Views: 4,398
Posted By ohofmann
The 'robust' list posted above is a good starting...

The 'robust' list posted above is a good starting point, with another vote for Novoalign. Completely depends on what your aims are -- we've added Mosaik to the list because we needed support for...
Forum: Bioinformatics 08-20-2009, 04:01 AM
Replies: 53
Views: 70,204
Posted By ohofmann
Somehow missed Martin's post, strange. Thanks for...

Somehow missed Martin's post, strange. Thanks for the pointer! And yes, the UCR pages are a great starting point.

-- Oliver
Forum: Bioinformatics 08-20-2009, 03:51 AM
Replies: 53
Views: 70,204
Posted By ohofmann
And a question related to the one above -- does...

And a question related to the one above -- does readAligned also support (or plans to support) the SAM format?
Forum: Bioinformatics 08-20-2009, 03:13 AM
Replies: 6
Views: 9,984
Posted By ohofmann
Should be 0.1; see...

Should be 0.1; see http://en.wikipedia.org/wiki/Phred_quality_score
Forum: Bioinformatics 08-18-2009, 07:08 AM
Replies: 10
Views: 2,936
Posted By ohofmann
No rush at all, and thanks! -- Oliver

No rush at all, and thanks!

-- Oliver
Forum: Bioinformatics 08-17-2009, 08:21 AM
Replies: 10
Views: 2,936
Posted By ohofmann
Aaron, not sure it's worth the hassle --...

Aaron,


not sure it's worth the hassle -- just adding the information to the man page should be more than enough. My current workflow, using the mapping of SNPs to genes within a 25kb window as...
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