User: hbw

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hbw70
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Posts by hbw

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Retrieve All Genes Associated With A Go Term
... This seems to give the genes only specifically annotated to the given GO term, and not any genes associated with the child terms. Mostly one is interested in ALL the genes for a GO term, i.e, with both direct and indirect annotations. ...
written 11 weeks ago by hbw70
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What problem does the MA plot diagnose? And how do you solve it?
... I have an RNASeq experiment, and I am using DESeq2. After I get the results, I plot the MA plot. This is the output of plotMA: ![DESeq2 MAplot][1] And this is my attempt at the MA plot: res$significant = (res$padj < .05) res$significant = as.factor(res$significant) res$significant[i ...
rna-seq written 2.3 years ago by hbw70 • updated 2.1 years ago by Biostar ♦♦ 20
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Comment: C: Units Of Dn And Ds In Codeml Paml Output
... So how can we get dS>1 for pairwise comparisons? ...
written 3.0 years ago by hbw70
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Answer: A: Estimating synonymous substitution rate
... Use paml and maybe infer a hypothetical ancestral sequence to calculate the substitution rates against. Think about which rate you actually want. Substitution since the most recent ancestor? Then you should organize the species in a phylogenetic tree. ...
written 3.0 years ago by hbw70
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Aligning AFLP primers
... I am trying to blast AFLP primer sequences to the genome to find the locations of the AFLP markers. However, I can't seem to find full alignments for the primers on the genome. For example, in the paper "AFLP fingerprinting of the human genome", Human Genetics,  108(1):59-65, Table 1 reports 100's ...
aflp genetics markers written 3.4 years ago by hbw70
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Answer: A: Organism portal framework
... Caleydo seems to be geared towards pathway analysis. ...
written 3.6 years ago by hbw70
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Comment: C: Genome Rearrangement Detection (From Short Reads Alignment Or Genome Alignment)
... Thanks! (+1). Will Sibelia work for larger organisms like plants? I also asked a similar question here. ...
written 3.6 years ago by hbw70
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Principled structural variation detection with assembled genomes or pacbio reads
... I want to compare my assembled genome with a reference for structural variation. Most SV methods map resequenced paired-end reads to the reference such as SVdetect, BreakDancer etc. However, my main source of long range information are pacbio reads. I have also done a hybrid assembly. I have two que ...
genome assembly smrt structural-variation pacbio written 3.6 years ago by hbw70 • updated 18 months ago by Biostar ♦♦ 20
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Organism portal framework
... I want to put up a portal for my relatively obscure organism. I will have my own genome, some gene annotations, some gene expression (RNA-seq) results, perhaps some proteomics data. The project does not justify a full time web developer. I am looking for some software which will let me host this in ...
genome written 4.2 years ago by hbw70
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Analysis and tools for gene/pathway conservation
... I am interested in looking at a number of genes in 2 or 3 closely related eukaryotic genomes. I think interesting questions to answer would be: Which subset among my genes is most conserved in all the genomes. Which set of genes show higher sequence similarity/conservation as compared to all ...
tools evolution written 4.2 years ago by hbw70

Latest awards to hbw

Popular Question 2.3 years ago, created a question with more than 1,000 views. For Inconsistent Cap3 Assembly
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Principled structural variation detection with assembled genomes or pacbio reads
Popular Question 2.3 years ago, created a question with more than 1,000 views. For What problem does the MA plot diagnose? And how do you solve it?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Good Poly-A Filtering Rules Or Tools
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Analysis and tools for gene/pathway conservation
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Database Of Cell Types, Division Rates, And Differentiation
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Inconsistent Cap3 Assembly
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Database Of Cell Types, Division Rates, And Differentiation
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Database Of Cell Types, Division Rates, And Differentiation
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Blast Gives Cryptic Errors
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Blast Gives Cryptic Errors

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