Moderator: Casey Bergman

gravatar for Casey Bergman
Casey Bergman17k
Reputation:
17,070
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Location:
Manchester, UK
Website:
http://bergman-lab.org/
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Google Scholar Page
Last seen:
1 year, 10 months ago
Joined:
7 years, 4 months ago
Email:
c************@manchester.ac.uk

Molecular Evolutionist turned Bioinformatician, working on various aspects of Genome Annotation, Genome Evolution, Functional Genomics and Text Mining.

 

Lab Blog, Lab Twitter, Personal Blog, Personal Twitter

 

 

Posts by Casey Bergman

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Answer: A: How To Get All Runs For A Sample In Sra?
... You can do this using CGI or REST interfaces from NCBI or EBI, respectively. From NCBI, use the SRA Run Info CGI $ wget -qO- 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term=SRS049712' | grep SRS049712 | cut -f1 -d"," SRR061165 SRR061174 From ...
written 23 months ago by Casey Bergman17k
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Job: Tenure Track Assistant/Associate Professor Position in Computational Plant Biology
... ASSISTANT/ASSOCIATE PROFESSOR POSITION IN COMPUTATIONAL PLANT BIOLOGY AT THE UNIVERSITY OF GEORGIA Job Summary: The University of Georgia invites applications at the Assistant/Associate Professor level for a tenure-track faculty position addressing the big data/data science challenges posed by C ...
jobs plant biology computational biology written 23 months ago by Casey Bergman17k
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Comment: C: Optimal design for bioinformatics "lab" space?
... Thanks for your comments, I think there are many bioinformaticians in this kind of setting, which I agree is not close to being optimal for the kind of work we do. Do you see any upside to being located inside a wet lab? ...
written 2.4 years ago by Casey Bergman17k
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Comment: C: Optimal design for bioinformatics "lab" space?
... Thanks for all these comments. Dan. I agree with all of them. I hadn't thought about the issue of glass walls, which I can see would lead to fewer interruptions. To put things in more context, how many people do you share your workspace with? ...
written 2.4 years ago by Casey Bergman17k
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Comment: C: Optimal design for bioinformatics "lab" space?
... LOL. I'm tempted to mark this as the answer. ...
written 2.4 years ago by Casey Bergman17k
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Answer: A: Optimal design for bioinformatics "lab" space?
... In Manchester to have dedicated bioinformatics space, with labs and PI offices interdigitated based on a design by Terrri Attwood who was involved with the planning of our building. The labs are 3.5mx5m (11.5ftx16.5ft) and hold up to 6 people. One door (solid with window) opens into the lab that can ...
written 2.4 years ago by Casey Bergman17k
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Forum: Optimal design for bioinformatics "lab" space?
... [ Cross posted on r/bioinformatics - some other good replies can be found there.] While much thought has been put into design for laboratory space and tech companies like Github have put substantial effort into office design for software engineering, most bioinformaticians I've seen (in universitie ...
lab space forum design written 2.4 years ago by Casey Bergman17k • updated 2.4 years ago by Yannick Wurm2.2k
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Comment: C: Application of Hi-C
... "Today's resolution allows you to split the genome into 0.5-1Mb regions and to get an estimate of contact frequency between a pair of regions on the same/different chromosomes." This statement is true for mammals, but much higher resolution (and deeper insight) can be obtained from Hi-C in Drosophi ...
written 2.6 years ago by Casey Bergman17k
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Answer: A: How to compute physical per-base coverage from WGS paired-end reads?
... You can do this in three steps using bedtools. First convert your paired-end BAM file to a BEDPE formated file of fragments with bedtools bamToBed, then use cut to convert BEDPE to BED, then use bedtools genomecov to compute coverage from the resulting BED file of fragments. See this the section aft ...
written 2.6 years ago by Casey Bergman17k
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Answer: A: Number Of Reads In A Sam File Which Are Assigned To Each Chromosome?
... The solution based on samtools idxstats aln.bam should be used with caution. This is because AFAIK the numbers reported by samtools idxstats (& flagstat) represent the number of alignments of reads that are mapped to chromosomes, not the (non-redundant) number of reads, as stated in the documen ...
written 2.7 years ago by Casey Bergman17k

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Prophet 2.4 years ago, created a post with more than 20 followers. For Optimal design for bioinformatics "lab" space?
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Scholar 2.6 years ago, created an answer that has been accepted. For A: How to compute physical per-base coverage from WGS paired-end reads?
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Great Question 2.7 years ago, created a question with more than 5,000 views. For What Are The Classic Papers In Bioinformatics?
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