User: erictleung

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erictleung90
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https://erictleung.com/
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@erictleung
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Posts by erictleung

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Bowtie2 parallelization on cluster
... You can use the `-p` option to specify the number of parallel search threads (see http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#performance-tuning for more performance information). The [manual](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml) in general has lots of good information ...
written 9 weeks ago by erictleung90
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Comment: C: SCDE Package error
... I haven't used `scde.error.models()` before, but I would guess it has to do with the `counts` or `groups` parameters. According to the documentation, `counts` should be > a read count matrix...the rows correspond to genes (should be named), columns correspond to individual cells. So I would ch ...
written 9 weeks ago by erictleung90
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Answer: A: SCDE Package error
... According to the warning you're getting ``` package 'scde' is not available (for R version 3.2.3) ``` looks like you'll want to upgrade your R version. Currently, R is at [3.4.1](https://www.r-project.org/). I'd upgrade R and Bioconductor both to see if that fixes your problem. Good luck. ...
written 9 weeks ago by erictleung90
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Answer: A: Does anyone know good open data sources for metagenomic data linked to a given
... The closest databases I can think of are - Repositive (https://discover.repositive.io/), which is more general purpose sequencing data - Qiita (https://qiita.ucsd.edu/), which is microbial sequencing specific - American Gut Project (http://americangut.org/), where some data can be found at https:// ...
written 9 weeks ago by erictleung90
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Answer: A: aligning with STAR
... An easy way to install STAR would be to use [Homebrew](http://brew.sh/), in case you don't already have it. It not only have Unix utilities you can download but there a plethora of [science tools also available](https://github.com/Homebrew/homebrew-science). Once you have Homebrew installed, install ...
written 15 months ago by erictleung90
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Answer: A: KEGG pathway mapping for metabolites
... You could look at programmatically searching for all 500 metabolites. Here are some places to look for ideas: - KEGG API http://www.kegg.jp/kegg/rest/keggapi.html - KEGG module in Biopython http://biopython.org/DIST/docs/api/Bio.KEGG-module.html - KEGGREST package in R's Bioconductor http://biocond ...
written 15 months ago by erictleung90
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Answer: A: Good Bioinformatics research papers
... There is a post on review papers compiled here on Biostars. Review papers generally have many pages and lots of citations so that should be sufficient for your class assignment. You asked for more of NGS technologies so this post is on sequencing technology review papers. Good luck. ...
written 22 months ago by erictleung90
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Answer: A: How to extract SNPs of Illumina Omniexpress from Denisovan data?
... Here is a very similar post to your question: https://www.biostars.org/p/77840/ Also, here's a list of various tools you can use to parse through VCF files to help get the information you need: https://kromozome.wordpress.com/2014/09/09/vcftools/ I hope this helps. ...
written 23 months ago by erictleung90
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Answer: A: Biopython Entrez difference between nuccore and nucleotide databases
... When trying to figure out the difference between the two databases, I also ran the same commands on the database descriptions, which indicates to me that they are the same database. In the Biopython tutorial under Chapter 9, it mentions "The Bio.Entrez module makes use of the Entrez Programming Uti ...
written 23 months ago by erictleung90

Latest awards to erictleung

Scholar 9 weeks ago, created an answer that has been accepted. For A: Biopython Entrez difference between nuccore and nucleotide databases
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Biopython Entrez difference between nuccore and nucleotide databases
Scholar 23 months ago, created an answer that has been accepted. For A: Biopython Entrez difference between nuccore and nucleotide databases

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