User: halo22

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halo22150
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150
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Indianapolis, IN
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M.S. Bioinformatics 

Posts by halo22

<prev • 54 results • page 1 of 6 • next >
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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 10 days ago by halo22150
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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 10 days ago by halo22150
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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 4 months ago by halo22150
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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 5 months ago by halo22150 • updated 4 months ago by chrchang5237.1k
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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 8 months ago by halo22150
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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 15 months ago by halo22150 • updated 9 months ago by Biostar ♦♦ 20
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Comment: C: Reading methylation without IDAT files downloaded from GEO
... Thank you! I will reach out to the person who uploaded the data and ask for IDAT's. ...
written 21 months ago by halo22150
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Reading methylation without IDAT files downloaded from GEO
... Hello All, I am working on a GEO series methylation dataset (GSE*) that I have downloaded from the GEO site. The downloads include three different files, 1) GSE*_Matrix_methylated_signal_intensities.txt.gz 2) GSE*_Matrix_methylated_signal_intensities.txt.gz 3) GSE*_RAW.tar, since there is no IDAT ...
geo methylation minfi gene expression omnibus written 21 months ago by halo22150 • updated 21 months ago by Charles Warden7.8k
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Turning transcript estimate to gene level estimates
... Hello All, I've used the featureCounts program on my bam files to estimate the transcript counts(below is the code snippet). Since a single gene can have multiple transcripts associated with it. What would be the best way to calculate a gene level estimate? Can adding gene specific transcript c ...
next-gen rna-seq written 23 months ago by halo22150 • updated 23 months ago by Devon Ryan95k
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Analyzing data produced by the UMI based SCRB-seq (Soumillon et al. 2014) protocol.
... Hello All, I am working on analyzing single cell RNA-seq data generated using the SCRB-seq protocol. The data that I have has already gone through data pre-processing including demultiplexing the BCL files using Picard, alignment with STAR, QC with RNASeqQC and marking duplicates with UmiAwareMarkD ...
next-gen rna-seq written 23 months ago by halo22150 • updated 22 months ago by Biostar ♦♦ 20

Latest awards to halo22

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Popular Question 4 months ago, created a question with more than 1,000 views. For Enrichr analysis using ranked gene list
Popular Question 4 months ago, created a question with more than 1,000 views. For Integrating WGS and RNA-seq data
Popular Question 4 months ago, created a question with more than 1,000 views. For Single cell RNA sequencing with Fluidigm vs Drop-seq?
Great Question 8 months ago, created a question with more than 5,000 views. For What is Digital Gene Expression?
Popular Question 8 months ago, created a question with more than 1,000 views. For Integrating WGS and RNA-seq data
Popular Question 8 months ago, created a question with more than 1,000 views. For Allele specific analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For What is Digital Gene Expression?
Popular Question 14 months ago, created a question with more than 1,000 views. For Single cell RNA sequencing with Fluidigm vs Drop-seq?
Popular Question 14 months ago, created a question with more than 1,000 views. For Integrating WGS and RNA-seq data
Popular Question 14 months ago, created a question with more than 1,000 views. For Time series comparison with DESEQ2
Popular Question 14 months ago, created a question with more than 1,000 views. For Comparing genes expression across samples in single cell RNA sequencing.
Popular Question 14 months ago, created a question with more than 1,000 views. For Help with Minfi for methylation analysis.
Popular Question 14 months ago, created a question with more than 1,000 views. For Enrichr analysis using ranked gene list
Popular Question 22 months ago, created a question with more than 1,000 views. For What is Digital Gene Expression?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Integrating WGS and RNA-seq data
Popular Question 2.2 years ago, created a question with more than 1,000 views. For What is Digital Gene Expression?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Single cell RNA sequencing with Fluidigm vs Drop-seq?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Single cell RNA sequencing with Fluidigm vs Drop-seq?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For What is Digital Gene Expression?
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