User: munch

gravatar for munch
munch300
Reputation:
300
Status:
New User
Location:
Munich
Last seen:
5 years, 4 months ago
Joined:
6 years, 1 month ago
Email:
r************@biostars.org

Master student of Clinical and Genetic Epidemiology (University of Munich)

B.Sc in Bioinformatics

Posts by munch

<prev • 27 results • page 1 of 3 • next >
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Classify Type Of Amino Acid Transitions (Acidic/Basic) Based On Their Mutations At Nucleotide Level
... I want to detect if there is in a multiple sequence alignment more basic to acidic or acidic to basic amino acid transitions based on their mutations at nucleotide level. For example: Basic: Histidine, Lysine, Arginine Acidic: Aspartate, Glutamate, Asparagine, Glutamine Is there any software pac ...
amino-acids multiple-alignment written 5.4 years ago by munch300 • updated 4.4 years ago by Biostar ♦♦ 20
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How To Filter Smith-Waterman Alignment (With Water From Emboss) According To Similarity Or Score?
... I make pairwise alignment with ./water form the emboss package. I want all fasta identifier of the sequences which align with a similarity of > 60%. I can find no option to set a threshold for the identity, similarity or the alignment score. I can parse the output, but maybe you have any tips her ...
similarity alignment filtering written 5.6 years ago by munch300 • updated 5.6 years ago by Ben2.0k
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High Variation Of Raw Intensities In Same Transcript Cluster In Gene Expression Array
... Without background correction and normalization, the spots of the same gene expression array have very high intensity variation on probe level. For example, the raw intensities on HuGene-1st-v1 (triplicate) the gene MSI2 vary between ~5300 and 27 for the same gene: probeID array1 array2 ...
affymetrix probeset written 5.8 years ago by munch300 • updated 5.8 years ago by Devon Ryan90k
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Comment: C: How To Get Probeset_Id From A Genefeatureset Object In R
... probeNames() from oligo worked. ...
written 5.8 years ago by munch300
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How To Filter Out Reads With A Bad Cigar M Operator
... My aim was to run freebayes on my .bam files generated with bwa, but I got the error: Error: cannot construct subsequence with negative offset or length < 1(attempting start = 66 and length = -8) So I think there is something wrong with my .bam file. The output of ValidateSamFile.jar from pica ...
cigar picard samtools bam written 5.9 years ago by munch300 • updated 5.9 years ago by KCC3.9k
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Comment: C: How To Annotate A Set Of Prokaryotic Genomes With Eggnog Orthologous Groups?
... Thank you, this will help me a lot! ...
written 6.0 years ago by munch300
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How To Annotate A Set Of Prokaryotic Genomes With Eggnog Orthologous Groups?
... Hello, Im working on a metagenomic analysis where I need a reference set consisting of ~1500 prokaryotic genomes (in fasta format) from MetaHit and GenBank. My aim is to annotate the genes in this genomes with eggNOG orthologous groups. From the eggNOG download site I think the dataset "Bacteria n ...
metagenomics orthologues written 6.0 years ago by munch300 • updated 6.0 years ago by sarahhunter600
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Comment: C: What Are Usual Logfc Values In Differential Ge Analysis?
... Thank you! They seem only partly seperated. I have changed the code to handle the problem when the variance is zero and to prevent the Error cannot rescale a constant/zero column to unit variance: library(scatterplot3d) pca_matrix <- t(exprs(eset)) variances <- apply(pca_matrix, 2, var) # ...
written 6.0 years ago by munch300
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Comment: C: What Are Usual Logfc Values In Differential Ge Analysis?
... thats the next problem. After multiple testing correction no gene is significant. ...
written 6.0 years ago by munch300
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What Are Usual Logfc Values In Differential Ge Analysis?
... Hello, I want compare GE from experiment A (three replicates) with experiment B (three replicates) Here is my workflow: library(limma) celFiles <- list.celfiles(path_to_cel_files,full.names=TRUE) affyExpressionFS <- read.celfiles(celFiles) eset <- rma(affyExpressionFS, background = TRUE ...
gene-expression limma written 6.0 years ago by munch300 • updated 6.0 years ago by Irsan6.8k

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