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Search: Posts Made By: danielsbrewer
Forum: Academic/Non-Profit Jobs 07-19-2019, 03:19 AM
Replies: 0
Views: 260
Posted By danielsbrewer
Research Associate in Genomics Pipelines @ UEA, Norwich, UK

We are looking for a Research Associate to implement, and then run, a resource within the Norwich Medical School to process next generation sequencing data using best-of-class bioinformatics...
Forum: Academic/Non-Profit Jobs 03-19-2018, 02:33 AM
Replies: 0
Views: 493
Posted By danielsbrewer
EU/UK funded PhD Studentship - Detecting novel subtypes of cancer using data science

Cancer is not a single disease but a collection of diseases arising in a wide range of tissues. Even within a single cancer type such as breast cancer there can be multiple forms. Identifying...
Forum: Academic/Non-Profit Jobs 12-20-2017, 07:40 AM
Replies: 0
Views: 713
Posted By danielsbrewer
PhD Studentship - Detecting novel cancer subtypes in The Cancer Genome Atlas datasets

More information: https://goo.gl/uMnFAH

Cancer is not a single disease but a collection of diseases in different tissues. Even within a single cancer type such as breast cancer, dividing up the...
Forum: Academic/Non-Profit Jobs 05-10-2017, 06:19 AM
Replies: 0
Views: 1,056
Posted By danielsbrewer
Development of a Test for Prostate Cancer : PhD Studentship @ UEA, Norwich

Biomarker Data Analysis: Development of a Test for Prostate Cancer : PhD Studentship @ UEA, Norwich, UK

Prostate cancer (PCa) is extremely common and has been detected in 30% of 40 year-old men,...
Forum: Academic/Non-Profit Jobs 05-10-2017, 06:13 AM
Replies: 0
Views: 915
Posted By danielsbrewer
Hunting for Human Infectious Agents in Cancer : PhD Studentship @ UEA, Norwich

Hunting for Human Infectious Agents in Cancer using data from Genomics England’s 100,000 genome project : PhD Studentship @ UEA, Norwich

Infectious agents, such as bacteria and viruses, are...
Forum: Academic/Non-Profit Jobs 03-01-2017, 06:56 AM
Replies: 0
Views: 721
Posted By danielsbrewer
Hunting for Human Infectious Agents in Cancer : PhD @ Norwich, UK

Hunting for Human Infectious Agents in Cancer using data from Genomics Englandís 100,000 genome project : PhD Studentship @ UEA, Norwich

Infectious agents, such as bacteria and viruses, are...
Forum: Academic/Non-Profit Jobs 08-15-2016, 03:33 AM
Replies: 0
Views: 1,057
Posted By danielsbrewer
2 year bioinformatics postdoc in the microbiome and prostate cancer risk @Norwich, UK

We are looking for a talented and motivated individual to join a dynamic, multi- disciplinary research team at the University of East Anglia in Norwich as a Bioinformatics Officer to work on the...
Forum: Academic/Non-Profit Jobs 02-29-2016, 12:47 AM
Replies: 0
Views: 1,473
Posted By danielsbrewer
2015 Movember Foundation PhD Studentship in Bioinformatics @ UEA, Norwich, UK

The Application of Genome DNA Sequencing Technologies and Bioinformatics to Understanding Why there are Multiple Areas of Cancer in Prostate Cancer Patients - 2015 Movember Foundation PhD Studentship...
Forum: Academic/Non-Profit Jobs 02-02-2016, 01:10 AM
Replies: 0
Views: 869
Posted By danielsbrewer
PhD: Detection of infectious agents in animal disease from WGS - Norwich, UK

PhD studentship - Detection of infectious agents in animal disease from whole genome sequencing data (COOPERU16HDTP)
University of East Anglia | Faculty of Medicine and Health Sciences | Norwich |...
Forum: Academic/Non-Profit Jobs 10-09-2015, 06:41 AM
Replies: 0
Views: 1,005
Posted By danielsbrewer
4 year PhD Bioinformatics studentship UEA/TGAC, UK

Competition-funded studentship: Class-seq: Detection of infectious agents in animal disease from whole genome sequencing data

Infectious agents are known to be involved in the development of a...
Forum: Academic/Non-Profit Jobs 08-17-2015, 06:39 AM
Replies: 0
Views: 620
Posted By danielsbrewer
Senior Research Associate in Bioinformatics, Norwich Medical School, UEA, UK

Senior Research Associate in Bioinformatics
REF: RA1220

Norwich Medical School
University of East Anglia

£31,342 to £37,394 per annum

This is a full time post funded by Hoffman La Roche...
Forum: RNA Sequencing 01-13-2014, 02:50 AM
Replies: 10
Views: 7,918
Posted By danielsbrewer
Yes that would have done the trick. Still...

Yes that would have done the trick. Still playing around with RNAseq data so I am definitely in the learning phase!

The script in the following looks like it will help:...
Forum: RNA Sequencing 01-13-2014, 02:49 AM
Replies: 10
Views: 7,918
Posted By danielsbrewer
Yes that would have done the trick. Still...

Yes that would have done the trick. Still playing around with RNAseq data so I am definitely in the learning phase!

The script in the following looks like it will help:...
Forum: RNA Sequencing 01-13-2014, 02:12 AM
Replies: 10
Views: 7,918
Posted By danielsbrewer
On further examination, it appears that the FLAGS...

On further examination, it appears that the FLAGS in the unmapped.bam are inaccurate and even after filtering out the reads without the unpaired flag, there are still reads that are unpaired. I...
Forum: RNA Sequencing 01-13-2014, 01:48 AM
Replies: 10
Views: 7,918
Posted By danielsbrewer
Tophat2: prepare unmapped.bam file for input into a tophat run on alternative genome

I have some paired-end Illumina RNAseq data and have run tophat2 on it against the human genome. I would like now like to run tophat2 again to align the unmapped bams on some alternative genomes to...
Forum: Bioinformatics 09-29-2011, 12:54 AM
Replies: 3
Views: 4,159
Posted By danielsbrewer
Many thanks for the reply. There are definitely...

Many thanks for the reply. There are definitely reads that have the flag 0x200. I have contacted Illumina (they generated the data) to ensure that I have got the right flag etc.
Thanks
Forum: Bioinformatics 09-29-2011, 12:50 AM
Replies: 6
Views: 6,108
Posted By danielsbrewer
SplitBam looks ideal, but I can't find a download...

SplitBam looks ideal, but I can't find a download link for it. Any ideas?

And thanks for the other suggestion too, that makes a lot of sense.

--EDIT--
Actually it looks like there are no @RG...
Forum: Bioinformatics 09-28-2011, 07:46 AM
Replies: 4
Views: 4,612
Posted By danielsbrewer
http://seqanswers.com/forums/showthread.php?t=4994

http://seqanswers.com/forums/showthread.php?t=4994
Forum: Bioinformatics 09-28-2011, 07:40 AM
Replies: 6
Views: 6,108
Posted By danielsbrewer
Convert merged BAM back to per lane BAM or FASTQ file

I have got some illumina data in a a merged BAM file for a particular sample and I would like to convert it back to per lane data files (BAM or fastq) so it would be compatible with the analysis...
Forum: Bioinformatics 09-28-2011, 07:33 AM
Replies: 3
Views: 4,159
Posted By danielsbrewer
Filtering a BAM by chastity flag using samtools

Dear all

I have a BAM file from Illumina whole genome data and I would like to filter out all the reads that fail Illumina's chastity filtering. From my understanding that is the flag 0x0200...
Forum: Bioinformatics 02-03-2011, 01:42 AM
Replies: 4
Views: 2,514
Posted By danielsbrewer
Convert CASAVA file to VCF

Are there any tools to convert from the CASAVA file format to VCF? I would like to be able to view the output in IGV but I am having problems. Newbie in this kind of thing.
Forum: General 09-23-2010, 12:33 AM
Replies: 3
Views: 2,495
Posted By danielsbrewer
Here is a list of the ones we have got already ...

Here is a list of the ones we have got already

CONAN (http://www.sanger.ac.uk/cgi-bin/genetics/CGP/conan/search.cgi)
Cancer Genome Workbench (https://cgwb.nci.nih.gov/)
Breast...
Forum: General 09-22-2010, 02:14 AM
Replies: 3
Views: 2,495
Posted By danielsbrewer
Sources of information about amplified genes (and overexpressed) in cancer

I was wondering whether anyone could suggest sources of information about amplified genes in cancer, especially if the website tries to combine it with (over)expression information. We wrote a...
Forum: Bioinformatics 06-02-2009, 02:14 AM
Replies: 1
Views: 1,291
Posted By danielsbrewer
Viral RNA sequence library

Hi,

I have got some Solexa data from cancer tissue mRNA (looking at length mRNA only) and I am interesting in looking at whether there is viral RNA within the reads. DOes anyone know whether...
Forum: Bioinformatics 03-10-2009, 01:59 AM
Replies: 3
Views: 4,230
Posted By danielsbrewer
I think I have worked out the problem. Novoalign...

I think I have worked out the problem. Novoalign outputs the source read sequence no matter what strand it is on whereas bowtie always takes the sequence on the same strand, no matter what strand...
Showing results 1 to 25 of 30

 


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