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Forum: Academic/Non-Profit Jobs 04-17-2019, 01:34 PM
Replies: 0
Views: 440
Posted By a11msp
Postdoctoral research associate - Cardiovascular genomics, Cambridge UK

We invite applicants for a three-year post-doctoral Research Associate post to undertake computational data analysis and potential related wet-lab work in the group of Dr Helle Jørgensen...
Forum: Academic/Non-Profit Jobs 06-13-2018, 04:15 AM
Replies: 0
Views: 1,518
Posted By a11msp
Lightbulb Postdoctoral Research Associate at MRC LMS in London

Postdoctoral positions are open in the newly established Functional Gene Control group at MRC London Institute for Medical Sciences (LMS) led by Dr Mikhail Spivakov...
Forum: Academic/Non-Profit Jobs 07-05-2014, 02:44 AM
Replies: 0
Views: 1,092
Posted By a11msp
Computational postdoc in Cambridge, UK: transcriptional regulation in 3D genome

http://www.babraham.ac.uk/jobs/transcriptional-regulation-in-3d-genome-computational-postdoctoral-research-scientist/

We are looking for a highly motivated computational postdoctoral scientist...
Forum: Academic/Non-Profit Jobs 01-21-2014, 01:49 AM
Replies: 0
Views: 1,400
Posted By a11msp
Bioinformatics postdoc at UCL Cancer Institute in London

Research Associate - Bioinformatics, - Ref:1395912

UCL Cancer Institute
Salary (inclusive of London allowance) £32,699 - £39,523 per annum

The Genome Organization and Function Group headed by...
Forum: Bioinformatics 10-16-2013, 03:48 AM
Replies: 5
Views: 2,402
Posted By a11msp
OK, thanks!

OK, thanks!
Forum: Bioinformatics 10-15-2013, 12:18 AM
Replies: 5
Views: 2,402
Posted By a11msp
Sorry, one more question... Am I right then that...

Sorry, one more question... Am I right then that for sharing mode == "maximum" and method == "per-condition", the maximum is computed between the fitted SCV given the overall mean and the observed...
Forum: Bioinformatics 10-01-2013, 08:32 AM
Replies: 5
Views: 2,402
Posted By a11msp
Thanks a lot for your reply Simon!

Thanks a lot for your reply Simon!
Forum: Bioinformatics 09-27-2013, 07:41 AM
Replies: 5
Views: 2,402
Posted By a11msp
A stats question about DESeq

It may be a slightly outdated question now that GLM-based testing is preferred to the exact test, but I'm just very curious...

In the 2010 Genome Biology paper...
Forum: Academic/Non-Profit Jobs 03-12-2013, 02:42 PM
Replies: 0
Views: 1,284
Posted By a11msp
Postdoctoral Research Scientist in Computational Genomics at Babraham Institute

Babraham Institute’s Nuclear Dynamics Programme is undertaking an ambitious BBSRC-funded project on the Systems Biology of Ageing in Haemopoiesis. As part of this project, we are generating...
Forum: Bioinformatics 04-23-2012, 06:33 AM
Replies: 0
Views: 3,317
Posted By a11msp
GATK error with a VCF including missing genotypes

Hello!

UPDATE: solved - was not to do with missing genotypes, but rather with triallelic SNPs that the tool cannot process.

I'm trying to phase my genotypes based on the data for 8 trios of a...
Forum: Bioinformatics 04-19-2012, 03:16 AM
Replies: 0
Views: 1,488
Posted By a11msp
Does bcftools produce phased genotypes?

Hi everyone,

I'm aware that samtools can produce phased genotypes using the phase option. Since I'm using trio designs (as some of you may have seen from my previous post...), I used bcftools...
Forum: Bioinformatics 04-17-2012, 02:50 AM
Replies: 0
Views: 1,862
Posted By a11msp
Calling genotypes on multiple trios

Hi everyone,

I have a set of eight Illumina-sequenced trios for an organism, for which a reference genome is available. I'd now like to call genotypes on these data taking advantage of both a...
Forum: Bioinformatics 11-21-2010, 05:29 AM
Replies: 2
Views: 2,130
Posted By a11msp
This is even better than what I was hoping to...

This is even better than what I was hoping to find, thanks a lot!
Forum: Bioinformatics 11-21-2010, 03:26 AM
Replies: 2
Views: 2,130
Posted By a11msp
pileup2vcf converter?

Hi everyone,

So not reinvent the wheel, I'm wondering if there are any existing tools that can convert samtools pileup -c format to VCF?

I notice it's long been listed as an open task here...
Forum: Bioinformatics 11-17-2010, 10:48 AM
Replies: 0
Views: 3,886
Posted By a11msp
samtools calmd -r

Dear colleagues,

I'm trying out samtools in the new calmd -r mode (compute base alignment quality) and since it's a very recent feature and not yet fully documented, just wanted to check whether...
Forum: Bioinformatics 10-14-2010, 04:22 AM
Replies: 4
Views: 9,583
Posted By a11msp
Thanks for your answer! I haven't heard of...

Thanks for your answer! I haven't heard of dindel, but I'm indeed trying SRMA and GATK indel realigner post-hoc. Will read up on dindel.
Forum: Bioinformatics 10-14-2010, 02:50 AM
Replies: 4
Views: 9,583
Posted By a11msp
Thanks for your reply!

Thanks for your reply!
Forum: Bioinformatics 10-13-2010, 04:10 PM
Replies: 7
Views: 2,047
Posted By a11msp
Yes, that's what I thought - so I don't assume...

Yes, that's what I thought - so I don't assume this is a minimally possible amount. It did freeze with 4Gb, however, so I wanted to stay on the safe side. Note that my dataset was 5-10x coverage of a...
Forum: Bioinformatics 10-13-2010, 03:56 PM
Replies: 7
Views: 2,047
Posted By a11msp
Hi Nils, thanks for your reply! Turns out, it's...

Hi Nils, thanks for your reply!
Turns out, it's hitting the wall on memory - unfortunately, without saying this explicitly.
I've just rerun it with -Xmx40G (sic!) and it takes ~45 mins to finish...
Forum: Bioinformatics 10-13-2010, 02:50 PM
Replies: 4
Views: 9,583
Posted By a11msp
Bowtie vs BWA: only 50% overlapping SNPs

Hi everyone,

I've run bowtie and bwa (using generally default parameters) on the same dataset and provisionally called SNPs using samtools pileup on each of them (without removing duplicates,...
Forum: Bioinformatics 10-13-2010, 01:32 PM
Replies: 7
Views: 2,047
Posted By a11msp
Can I just add that I also compiled a C version...

Can I just add that I also compiled a C version and it terminates almost immediately with the following error:


************************************************************
In function...
Forum: Bioinformatics 10-13-2010, 10:21 AM
Replies: 7
Views: 2,047
Posted By a11msp
SRMA freezes after 1/10 run

Hi everyone,

I'm trying out srma on bowtie and bwa aligned data and while I've
managed to successfully get round two initial problems, I'm stuck on
the third one:
Basically, srma works quite...
Forum: Bioinformatics 08-02-2010, 06:36 AM
Replies: 3
Views: 3,712
Posted By a11msp
Thanks to both of you for the suggestions! I...

Thanks to both of you for the suggestions!
I think I'll follow the route suggested by adamdeluca and convert my SNP tables to a series of bed files
Forum: Bioinformatics 07-30-2010, 06:02 AM
Replies: 3
Views: 3,712
Posted By a11msp
SNP visualisation

Hi everyone,

I'm wondering if there's a consensus of what tools to use to visualise SNPs.
I have the data in the form of a SNP table across a number of individuals, and my wet-lab collaborators...
Forum: Bioinformatics 06-24-2010, 02:36 AM
Replies: 2
Views: 2,832
Posted By a11msp
Ok, this has now been resolved. Turns out I was...

Ok, this has now been resolved. Turns out I was explicitly specifying the -v option with samtools pileup that excluded from the output all positions matching to the reference....
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