User: Cliff Beall

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Cliff Beall440
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Posts by Cliff Beall

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Job: Research Associate Microbiome Informatics - Ohio State University, Columbus, OH, USA
... Research Associate in Bioinformatics of the Oral Microbiome, Ohio State University The laboratory of Drs. Eugene Leys and Ann Griffen in the Division of Biosciences, College of Dentistry at the Ohio State University has an opening for a research associate to study the oral microbiome. We have sever ...
oral ohio job microbiome written 3 months ago by Cliff Beall440 • updated 3 months ago by genomax37k
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Answer: A: Understanding NCBI identifiers
... Those are almost the same protein sequence from the same organism but not exactly. It might be repeated genes, alternative splicing, variation between individuals, or even sequencing errors. nr is meant to be non-redundant so it will have an entry for every different protein that someone put into ...
written 14 months ago by Cliff Beall440
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Answer: A: Genomic assembly with spades
... Ok, actually it will only use Nanopore as part of a hybrid assembly. From the docs: "SPAdes should not be used if only PacBio CLR, Oxford Nanopore, Sanger reads or additional contigs are available." So it's expecting the nanopore reads filename after the --nanopore argument (which explains your er ...
written 18 months ago by Cliff Beall440
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Comment: C: Genomic assembly with spades
... Maybe give the error message or describe how it fails? ...
written 18 months ago by Cliff Beall440
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Comment: C: Position 1 in closed circular genome.
... Thanks, that is useful. Based on that I will treat the GC skew estimate as approximate and go with dnaA. I do see three repeats that might bind DnaA in the region between the gene and rpmH as well. ...
written 20 months ago by Cliff Beall440
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Comment: C: Position 1 in closed circular genome.
... Thanks, I hadn't found that question. It prompted me to look for the rpmH gene by tblastn, which turned out had been missed just upstream of dnaA. ...
written 20 months ago by Cliff Beall440
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Position 1 in closed circular genome.
... Dear BioStars I have managed to get a bacterial genome as a single contig. In looking at existing genomes, I notice that many of them have nucleotide #1 either as the beginning of the dnaA gene or a short distance upstream (perhaps at the actual origin?). On my genome I tried predicting the origin ...
genome bacteria written 20 months ago by Cliff Beall440 • updated 20 months ago by natasha.sernova2.6k
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Comment: C: Extracting rRNA sequences from illumina metagenomic dataset
... 61 reads out of 110,000 might not be too far off what you expect. I have had 1 in 1,000 reads from a metagenome map to SSU rRNA, and that was after removal of the human sequences from an oral sample. Although maybe you left off a digit or two from the number of starting reads? ...
written 2.5 years ago by Cliff Beall440
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Job: Postdoc in Bioinformatics of the Oral Microbiome, Ohio State University
... The laboratory of Drs. Eugene Leys and Ann Griffen in the Division of Biosciences, College of Dentistry at the Ohio State University has an opening for a postdoctoral associate to study the oral microbiome. We have several ongoing projects including studies of the acquisition of the oral microbiome ...
ohio state postdoc oral job microbiome written 2.5 years ago by Cliff Beall440
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Answer: A: As an illumina customer, do you use basespace, alternative cloud solution or pip
... I played around with the basespace applications a bit and was pretty unimpressed. From my experience it's not up to the task, though I'm not doing the same applications as you. For one example, the 16S analysis. It is pretty basic and inaccurate but I thought might give a preliminary idea of our sa ...
written 2.8 years ago by Cliff Beall440

Latest awards to Cliff Beall

Popular Question 11 months ago, created a question with more than 1,000 views. For Postdoc in Bioinformatics of the Oral Microbiome, Ohio State University
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: HIV : gtf or gff annotation
Popular Question 18 months ago, created a question with more than 1,000 views. For Biopython Seqio - Why Is It Repeating Deflines?
Popular Question 18 months ago, created a question with more than 1,000 views. For Differences of Bacterial Genome ftp folders at NCBI
Scholar 18 months ago, created an answer that has been accepted. For A: List Of Genome Sequencing Centers/Institutes
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: HIV : gtf or gff annotation
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Scholar 2.9 years ago, created an answer that has been accepted. For A: List Of Genome Sequencing Centers/Institutes
Scholar 2.9 years ago, created an answer that has been accepted. For A: List Of Genome Sequencing Centers/Institutes
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Looking For More Data To Build A Bacterial Primer Database
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Looking For More Data To Build A Bacterial Primer Database
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Looking For More Data To Build A Bacterial Primer Database
Student 3.7 years ago, asked a question with at least 3 up-votes. For Biopython Seqio - Why Is It Repeating Deflines?

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