User: mark.dunning

gravatar for mark.dunning
mark.dunning210
Reputation:
210
Status:
Trusted
Location:
The University of Sheffield
Website:
http://sbc.shef.ac.uk/
Twitter:
@DrMarkDunning
Last seen:
1 week, 1 day ago
Joined:
8 years, 1 month ago
Email:
m***********@gmail.com

Bioinformatics Core Director

The University of Sheffield

Posts by mark.dunning

<prev • 23 results • page 1 of 3 • next >
0
votes
0
answers
55
views
0
answers
Get data from SRA with just SAMN IDs
... Hi, We have student that would like to analyse and RNA-seq data for a project. According to the publication, the fastq files are open access and available https://pubmed.ncbi.nlm.nih.gov/28511992/ However, the only IDs I can find are "SAMN". https://www.ncbi.nlm.nih.gov/biosample?Db=biosample&a ...
ncbi sra fastq rna-seq written 8 days ago by mark.dunning210
0
votes
1
answer
890
views
1
answers
Comment: A: rRNA removal needed for salmon / DESeq2 analysis
... So the transcript file I was planning to use from Gencode does include rRNA sequences that I will have to remove before calling salmon ...
written 18 months ago by mark.dunning210
0
votes
1
answer
890
views
1
answers
Comment: C: rRNA removal needed for salmon / DESeq2 analysis
... Thanks! That seems like sensible advice. ...
written 18 months ago by mark.dunning210
4
votes
1
answer
890
views
1
answer
rRNA removal needed for salmon / DESeq2 analysis
... Hi all, I am re-analysing some RNA-seq data that I'm told have high levels of rRNA contamination (not sure how high yet). My usual workflow is salmon -> tximport -> DESeq2 I've seen recommendations that any reads matching rRNA need to removed prior to analysis. Is this still the case with th ...
rrna deseq2 salmon contamination written 18 months ago by mark.dunning210 • updated 6 months ago by ATpoint34k
0
votes
0
answers
414
views
0
answers
downloading zebrafish snps for annovar
... Hi, I am hoping to use annovar to annotate some zebrafish genome coordinates, and would like to incorporate snp positions. I can download reference sequences with the following retrieve_seq_from_fasta.pl tmp/danRer11_refGene.txt -seqdir tmp/danRer11_seq -format refGene -outfile tmp/danRer11_ ...
annovar zebrafish written 19 months ago by mark.dunning210
2
votes
0
answers
846
views
0
answers
Job: Sheffield Bioinformatics Core Analyst
... The Bioinformatics Core at The University of Sheffield is looking for an Analyst with strong statistical skills and awareness of best-practices and reproducible research. Please see below for a summary and how to apply **Summary** The University of Sheffield and its associated Medical School and H ...
job written 2.5 years ago by mark.dunning210
2
votes
0
answers
733
views
0
answers
Job: Sheffield Bioinformatics Core Analyst, The University of Sheffield, Sheffield, UK
... The University of Sheffield is launching a Bioinformatics Core, and we are looking for an Analyst to join the team If you have a passion for working with best practice Bioinformatics, promoting open science, and want to work in an awesome city, check it out! http://www.jobs.ac.uk/job/BDQ610/sheffi ...
bioinformatics core job analyst written 2.8 years ago by mark.dunning210 • updated 2.8 years ago by genomax83k
2
votes
0
answers
816
views
0
answers
Job: Sheffield Bioinformatics Core Analyst, University of Sheffield, Sheffield, UK
... The Bioinformatics Core at The University of Sheffield is looking for an Analyst. If best-practice Bioinformatics and reproducible research is your thing, check-out the full details below:- http://www.jobs.ac.uk/job/BBM484/sheffield-bioinformatics-core-analyst/ ...
bioinformatics core job written 3.0 years ago by mark.dunning210 • updated 3.0 years ago by genomax83k
0
votes
2
answers
1.6k
views
2
answers
Comment: C: Link to TCGA mutation calling benchmark dead?
... Did you manage to find them? I used these data in a workshop recently and wanted to give the link to where to download the data, only to find they had disappeared! ...
written 3.8 years ago by mark.dunning210
3
votes
0
answers
1.0k
views
0
answers
News: European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
... Dear Bioconductors, We are pleased to announce that that European Bioconductor Developers Conference will take place in Cambridge, England from 7th-8th December 2015. The meeting is aimed at bioinformaticians, programmers and software engineers who contribute to the Bioconductor project, or are in ...
news conference bioconductor written 4.7 years ago by mark.dunning210

Latest awards to mark.dunning

Popular Question 11 months ago, created a question with more than 1,000 views. For European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Tea Pipeline For Hg19
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Vcftools Get-Info Output Name
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Why Doesn'T Annovar With Dbsnp 129 Filter Anything
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Genome Music - Pathway File
Student 4.7 years ago, asked a question with at least 3 up-votes. For Genome Music - Pathway File
Popular Question 6.9 years ago, created a question with more than 1,000 views. For Why Doesn'T Annovar With Dbsnp 129 Filter Anything
Popular Question 6.9 years ago, created a question with more than 1,000 views. For Genome Music - Pathway File
Popular Question 6.9 years ago, created a question with more than 1,000 views. For Ngsrich Output Explanation
Teacher 6.9 years ago, created an answer with at least 3 up-votes. For A: Genome Music - Pathway File
Student 6.9 years ago, asked a question with at least 3 up-votes. For Genome Music - Pathway File

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 822 users visited in the last hour