User: Cliff Beall

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Cliff Beall450
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Posts by Cliff Beall

<prev • 60 results • page 1 of 6 • next >
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Answer: A: SNP Analysis of bacterial genomes
... A possible workflow would be trim with Trimmomatic, assemble with SPAdes, check the assemblies with Quast and then submit to IMG/MER - they have a tool that could determine average nucleotide identity to other Acinetobacter genomes and to each other. I would expect random isolates to have ANI in 95- ...
written 10 weeks ago by Cliff Beall450
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Comment: C: How to repair *all* problems identified by FastQC?
... Nextera genomic libraries also fail the "per base sequence content", at least they did a few years back. I believe that was because of some residual transposase bias in the first 10-15 bp. ...
written 10 weeks ago by Cliff Beall450
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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 6 months ago by Cliff Beall450 • updated 6 months ago by GenoMax42k
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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 17 months ago by Cliff Beall450
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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 21 months ago by Cliff Beall450
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Comment: C: Genomic assembly with spades
... Maybe give the error message or describe how it fails? ...
written 21 months ago by Cliff Beall450
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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 23 months ago by Cliff Beall450
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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 23 months ago by Cliff Beall450
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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 23 months ago by Cliff Beall450 • updated 23 months ago by natasha.sernova2.8k
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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 2.7 years ago by Cliff Beall450

Latest awards to Cliff Beall

Popular Question 14 months ago, created a question with more than 1,000 views. For Postdoc in Bioinformatics of the Oral Microbiome, Ohio State University
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: HIV : gtf or gff annotation
Popular Question 21 months ago, created a question with more than 1,000 views. For Biopython Seqio - Why Is It Repeating Deflines?
Popular Question 21 months ago, created a question with more than 1,000 views. For Differences of Bacterial Genome ftp folders at NCBI
Scholar 21 months ago, created an answer that has been accepted. For A: List Of Genome Sequencing Centers/Institutes
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: HIV : gtf or gff annotation
Supporter 2.2 years ago, voted at least 25 times.
Scholar 3.1 years ago, created an answer that has been accepted. For A: List Of Genome Sequencing Centers/Institutes
Scholar 3.2 years ago, created an answer that has been accepted. For A: List Of Genome Sequencing Centers/Institutes
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Looking For More Data To Build A Bacterial Primer Database
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Looking For More Data To Build A Bacterial Primer Database
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Looking For More Data To Build A Bacterial Primer Database
Student 3.9 years ago, asked a question with at least 3 up-votes. For Biopython Seqio - Why Is It Repeating Deflines?

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