User: LRStar

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LRStar0
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Posts by LRStar

<prev • 21 results • page 1 of 3 • next >
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Functional annotation chart from DAVID: Analogs or direct affiliations?
... I am trying to determine if genes I am examining are honey bee affiliations or are human analogs. Basically, I: 1) Went to the DAVID bioinformatics software (https://david.ncifcrf.gov/). 2) Used "functional annotation" option. 3) Input a list of BeeBase IDs (all beginning with "GB", such as "GB ...
annotation david functional written 4 days ago by LRStar0
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Comment: C: Mapping metagenome information to amplicon sequences
... Thanks for your advice! I did now use **bowtie2 --sensitive-local** for my samples (n=35). The 35 samples varied widely in terms of their total alignment, ranging between 0.09% and 94% alignment! Much of the reads that aligned did so to more than one location, with 1-time alignment ranging between ...
written 6 months ago by LRStar0
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Mapping metagenome information to amplicon sequences
... Hello all, I have a set of amplicon sequences for antimicrobial resistance determinants. Each amplicon sequence varies in length between 125 and 275 bp. I also have a .fastq file with metagenomic reads. Each metagenomic read varies in length between 25 and 473 bp. I would like to map the amplico ...
ampliseq mapper written 6 months ago by LRStar0 • updated 6 months ago by btsui290
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GeneID to BeeBaseID
... Hello all, Are there any steps one might take to try to determine the BeeBaseID (starting with 'GB') for a given Gene ID? The Gene ID of interest for me is 494510 (Apid22), and I am hoping to determine its corresponding BeeBaseID. I did try to use DAVID Bioinformatics software, which did successfu ...
genome written 6 months ago by LRStar0
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Statistical test for patterns in differentially expressed genes compared to variable
... I recently performed RNA-seq of 24 samples. 12 samples were healthy and 12 samples had been exposed to a chemical. For each of the 24 samples, the titer of this chemical was measured 24 hours after administration (and just before the RNA was extracted). I got a rather small list of DEGs (say n=100) ...
rna-seq written 9 months ago by LRStar0
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Comment: C: Convert Gene IDs into ENTREZ or ENSEMBL format (honey bee / apis mellifera)
... Thanks, Denise. Just checking, but how should I interpret this Error then if it seems I am providing the correct information? ...
written 12 months ago by LRStar0
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Preparing RNA-seq data for Hierarchical Clustering
... I am clustering RNA-seq data into groups of similar expression patterns and visualizing the results. To this end, I have been: 1) Logging and normalizing the RNA-seq data with the following two methods (first is from edgeR package, second is from EDASeq package) cpm.data.new <- cpm(data, TR ...
rna-seq written 12 months ago by LRStar0 • updated 12 months ago by Kevin Blighe37k
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Convert Gene IDs into ENTREZ or ENSEMBL format (honey bee / apis mellifera)
... Hello, I am trying to use the getGeneLengthAndGCContent() function from the EDASeq R package to obtain gene lengths and GC content for each gene in a honeybee (apis mellifera) dataset. An example subset of these genes are as follows: "GB40001" "GB40002" "GB40003" "GB40004" "GB40005" "GB40006" ...
ensembl entrez rna-seq written 15 months ago by LRStar0 • updated 15 months ago by Emily_Ensembl17k
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Comment: C: How is logFC and p-value estimated (for volcano plots)?
... I used a normalized version of my data. Thank you. ...
written 18 months ago by LRStar0
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How is logFC and p-value estimated (for volcano plots)?
... I am trying to understand how volcano plots are made in DEG studies. Say I have an example data frame that begins with the following first three rows: > head(myDF) ID C_S1_R1 C_S1_R2 C_S1_R3 C_S2_R1 C_S2_R2 C_S2_R3 1 Glyma0002s50.1 4.9191791 5.2691071 4.88150 ...
R foldchange edger written 23 months ago by LRStar0 • updated 11 months ago by jha.barkha810

Latest awards to LRStar

Great Question 6 months ago, created a question with more than 5,000 views. For Preparing a .genome file for snpEff
Popular Question 6 months ago, created a question with more than 1,000 views. For Terminology question: Phylogenetic tree duplicated generation counts
Popular Question 9 months ago, created a question with more than 1,000 views. For Terminology question: Phylogenetic tree duplicated generation counts
Epic Question 12 months ago, created a question with more than 10,000 views. For Convert .Gff3 File To 12-Column .Bed File
Popular Question 12 months ago, created a question with more than 1,000 views. For Terminology question: Phylogenetic tree duplicated generation counts
Great Question 2.8 years ago, created a question with more than 5,000 views. For Convert .Gff3 File To 12-Column .Bed File
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Convert .Gff3 File To 12-Column .Bed File
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Convert .Gff3 File To 12-Column .Bed File

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