User: Chris S.

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Chris S.300
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Posts by Chris S.

<prev • 33 results • page 1 of 4 • next >
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Answer: A: ERROR: failed to find the gene identifier attribute in the 9th column of the pro
... `featureCounts` does not allow empty values in the gene_id field, so you need to remove or update them. See this answer from the developer https://groups.google.com/g/subread/c/xs7mw38Bc6g. grep 'gene_id ""' GCF_003254395.2_Amel_HAv3.1_genomic.gtf grep -v 'gene_id ""' GCF_003254395.2_Ame ...
written 4 weeks ago by Chris S.300
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Comment: C: Why would there be a large bias in number in the negative and positive strand af
... I'm working with the same kit and get the same results using trim_galore with --paired and bismark with bowtie2 and -N 1 (directional is the default). No idea why... ...
written 2.1 years ago by Chris S.300
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Answer: A: FASTA file with taxid, want to obtain lineage and put into header
... There is a `rankedlineage.dmp` file in the `new_taxdump` directory at NCBI that has these ranks. wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz tar -zxvf new_taxdump.tar.gz Here's one way to format the file using R and tidyverse packages (and you'll still ne ...
written 2.4 years ago by Chris S.300
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Comment: C: Create a presence absence matrix in R for gene data
... and `(mat != "N/A")*1` will get 0s and 1s ...
written 4.3 years ago by Chris S.300
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Answer: A: Dividing Taxonomy Table in R
... If you have a table, try using the `tidyr` package x <- read.csv(text='id,taxa 1,"d:Bacteria(96.3),p:Firmicutes(70.8),c:Clostridia(69.2),o:Clostridiales(69.2),f:Lachnospiraceae(63.3),g:Roseburia(48.4)" 2,"d:Bacteria(93.3),p:Firmicutes(60.8),c:Bacilli(59.2),o:Bacillales(59.2),f:Bacill ...
written 4.3 years ago by Chris S.300
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Answer: A: Is there a way to know sequences length when querying ENA programmatically?
... The Paired nominal length does not seem to work in the ENA query builder here or at least it doesn't autofill into the query box, but you can add it to the URL string.  For example,  in the query builder, select domain = read and Library layout= Paired and optionally a taxon name like Bacteria , the ...
written 5.6 years ago by Chris S.300
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Answer: A: List of Lists to Table R
... You could try to rbind your list, then select the ranks you want, and reshape using one of the many available methods here.   Maybe something like... y <- ldply(x, "rbind", .id="species") z <-subset(y, rank %in% c("phylum", "order", "family") ) dcast(z, rank~species, value.var="name")   ...
written 5.7 years ago by Chris S.300
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Answer: A: How can one retrieve the list of PMIDs of abstracts associated with a MeSH term?
... Entrez Direct is another option esearch -db pubmed -query "Burkholderia pseudomallei/metabolism[MESH]" | efetch -format uid 24866793 24626296 24595140 24502667 24462575 ...       ...
written 5.7 years ago by Chris S.300
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Answer: A: discrepancy between t-test results in Excel and R
... You should also read a few papers that discuss problems with t-tests and other statistics in Excel, for example Heiser 2006. Statistical tests, tests of significance, and tests of a hypothesis using Excel. Journal of Applied Statistical Methods, 5:155–171  or McCullough and Heiser 2008. On the accur ...
written 5.7 years ago by Chris S.300
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Answer: A: Extract only viridiplantae genes form swissprot
... Just search UniProt for taxonomy:viridiplantae AND reviewed:yes to limit to SwissProt.  Click download to get FASTA and other formats as well as the REST url to reuse in your favorite application. ...
written 5.7 years ago by Chris S.300

Latest awards to Chris S.

Scholar 2.4 years ago, created an answer that has been accepted. For A: Entire Pubmed full text
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Using bowtie2 to create BAM files to view strand-specific coverage in Artemis
Scholar 5.6 years ago, created an answer that has been accepted. For A: Entire Pubmed full text
Scholar 5.7 years ago, created an answer that has been accepted. For A: Entire Pubmed full text
Scholar 5.7 years ago, created an answer that has been accepted. For A: Entire Pubmed full text
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Entire Pubmed full text
Scholar 6.0 years ago, created an answer that has been accepted. For A: Entire Pubmed full text
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Entire Pubmed full text

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