User: LRStar

gravatar for LRStar
LRStar10
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10
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New User
Location:
United States
Last seen:
2 months, 4 weeks ago
Joined:
5 years ago
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l**********@gmail.com

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Posts by LRStar

<prev • 20 results • page 1 of 2 • next >
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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 12 weeks ago by LRStar10
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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 3 months ago by LRStar10 • updated 3 months ago by btsui280
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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 3 months ago by LRStar10
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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 5 months ago by LRStar10
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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 9 months ago by LRStar10
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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 9 months ago by LRStar10 • updated 9 months ago by Kevin Blighe32k
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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 12 months ago by LRStar10 • updated 12 months ago by Emily_Ensembl16k
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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 15 months ago by LRStar10
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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 19 months ago by LRStar10 • updated 8 months ago by jha.barkha810
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Comment: C: Terminology question: Phylogenetic tree duplicated generation counts
... Thank you, David. I see what you mean about me misnaming it as phylogenetic. The visualization that I am thinking of, then, is a visualization of a simple cyclic graph, where the nodes are constrained by edge distance from the root node. Do you think that is the most standardized/eloquent/specific w ...
written 3.9 years ago by LRStar10

Latest awards to LRStar

Popular Question 5 months ago, created a question with more than 1,000 views. For Terminology question: Phylogenetic tree duplicated generation counts
Epic Question 9 months ago, created a question with more than 10,000 views. For Convert .Gff3 File To 12-Column .Bed File
Popular Question 9 months ago, created a question with more than 1,000 views. For Terminology question: Phylogenetic tree duplicated generation counts
Great Question 2.6 years ago, created a question with more than 5,000 views. For Convert .Gff3 File To 12-Column .Bed File
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Convert .Gff3 File To 12-Column .Bed File
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Convert .Gff3 File To 12-Column .Bed File

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