User: halo22

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halo22180
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Indianapolis, IN
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M.S. Bioinformatics 

Posts by halo22

<prev • 58 results • page 1 of 6 • next >
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Trimmomatic(0.39) java error [Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1]
... Hello All, I am trying to use Trimmomatic-0.39 to perform trimming on miRNA generated using the Truseq small rna library prep kit. I've downloaded the trimmomatic package in the same folder as the FASTQ's. I've also downloaded the adapter sequence file TruSeq3-SE.fa and placed under the same fold ...
sequence written 4 weeks ago by halo22180
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Answer: A: RNAseq Variance calculation
... I think you should look into variance stabilizing transformations (VST) and regularized logarithm or rlog first, a great place to start is the DESeq2 vignette (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html). VST and rlog both provide log2 transformed normalized va ...
written 3 months ago by halo22180
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Regression Analysis between RNA-seq data and expression measured from ELISA
... Hello All, I am trying to run a regression analysis on RNA-seq expected counts generated using RSEM. To perform the analysis I performed TMM normalization and extracted CPM values. I then used voomWithQualityWeights, lmFit and eBayes to perform association analysis. Since RNA has a different data d ...
rna-seq written 3 months ago by halo22180
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Ancestry prediction for non-related samples from a VCF file
... Hello All, I am trying to perform ancestry prediction for a set of non-related individuals and it seems that the tool peddy (https://github.com/brentp/peddy) would be a very easy option. Since these are unrelated samples, creating a PED file is meaningless. Is there a way to run peddy just for the ...
ancestry next-gen peddy sequencing written 3 months ago by halo22180
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Comment: C: DESeq2 Anova type comparison and Pvalues.
... Thanks, @Asaf. I went through the vignette and found that 'LRT' would give a P-value if there is any difference between groups. Wald is exactly what I was looking for. ...
written 5 months ago by halo22180
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DESeq2 Anova type comparison and Pvalues.
... Hello All, I am trying to make a group-wise comparison between 4 groups using DESeq2. After writing the contrast for the group comparisons, I see that log2foldchange and the lfcSE are different for each comparison but values for stat and p-value are the same for each comparison. Eg: Group1_vs_Group ...
deseq2 rna rna-seq written 5 months ago by halo22180
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Comment: C: Tool to check what alternate allele is dominant across samples per line of the V
... Thank you, guys! I wrote my own to get this done. ...
written 9 months ago by halo22180
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Tool to check what alternate allele is dominant across samples per line of the VCF file.
... Hello All, I am very new to WGS analysis. I have a multisample VCF file that I have annotated using snpEFF. I wanted to see if I can find what alternate alleles are conserved between samples for each genomic location. For eg: Chr1 pos: 1001, has a reference A and the alternate allele seen are T, ...
wgs next-gen written 10 months ago by halo22180 • updated 9 months ago by chrchang5237.4k
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GC overhead error [java.lang.OutOfMemoryError] while running snpEFF version 4.1
... Hello All, I am trying to run SnpEff on a multisample VCF file, the program processes variants until chr-5 and then dies with the following error. I'd really appreciate if you could help me with this. NOTE: I have added '-c snpEff.config" because I have edited the config file for the download an ...
next-gen snpeff written 13 months ago by halo22180
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How to use limma for a categorial outcome variable? Where outcome is the cohort status and predictor is gene expression.
... Hello All, I am very new to limma and trying to build a logistic regression like model using limma where my goal is to understand associations between the cohort status and gene expression while accounting for variables like age and sex. My gene expression is quantified using RSEM with TPM counts. ...
next-gen rna limma rna-seq written 20 months ago by halo22180 • updated 14 months ago by Biostar ♦♦ 20

Latest awards to halo22

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Integrating WGS and RNA-seq data
Popular Question 3 months ago, created a question with more than 1,000 views. For Enrichr analysis using ranked gene list
Student 3 months ago, asked a question with at least 3 up-votes. For How To Parse Data From An Owl File
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Popular Question 9 months ago, created a question with more than 1,000 views. For Enrichr analysis using ranked gene list
Popular Question 9 months ago, created a question with more than 1,000 views. For Integrating WGS and RNA-seq data
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Great Question 13 months ago, created a question with more than 5,000 views. For What is Digital Gene Expression?
Popular Question 13 months ago, created a question with more than 1,000 views. For Integrating WGS and RNA-seq data
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Popular Question 18 months ago, created a question with more than 1,000 views. For Single cell RNA sequencing with Fluidigm vs Drop-seq?
Popular Question 18 months ago, created a question with more than 1,000 views. For Integrating WGS and RNA-seq data
Popular Question 18 months ago, created a question with more than 1,000 views. For Time series comparison with DESEQ2
Popular Question 18 months ago, created a question with more than 1,000 views. For Comparing genes expression across samples in single cell RNA sequencing.
Popular Question 18 months ago, created a question with more than 1,000 views. For Help with Minfi for methylation analysis.
Popular Question 18 months ago, created a question with more than 1,000 views. For Enrichr analysis using ranked gene list
Popular Question 2.2 years ago, created a question with more than 1,000 views. For What is Digital Gene Expression?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Integrating WGS and RNA-seq data
Popular Question 2.6 years ago, created a question with more than 1,000 views. For What is Digital Gene Expression?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Single cell RNA sequencing with Fluidigm vs Drop-seq?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Single cell RNA sequencing with Fluidigm vs Drop-seq?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For What is Digital Gene Expression?
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