User: ResearchR

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ResearchR70
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Posts by ResearchR

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Mutect2 (GATK4, Java8) outputs empty VCF file for tumor only mode
... I found the solution to my problem....you have to use `-outSAMmapqUnique 60` in STAR to make GATK software work with your output. @igor: Thanks for the reply!! ...
written 3 months ago by ResearchR70
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Mutect2 (GATK4, Java8) outputs empty VCF file for tumor only mode
... Dear all, I am using Mutect2 (GATK4 with Java 8, OpenJDK) on RNA-Seq data from a tumor. I would like to call SNVs (as part of a RNA editing pipeline), but Mutect2 outputs always an empty SNV file. I went through the GATK forum since this problem occurred quite often for the GATK3 version of the too ...
snv rna-seq mutect2 written 3 months ago by ResearchR70 • updated 3 months ago by RamRS24k
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Answer: A: Differential Expression between 3 groups ?
... I never used *edgeR*, but in *DESeq2* you can specify multiple conditions as factor in the model formula. What you maybe could do, is to run test like "C1 vs Normal" and "C2 vs Normal" and see which genes appear to be diff. expressed in both conditions. Of course, it might happen that genes are also ...
written 4 months ago by ResearchR70
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Comment: C: Testing Distances in Phylogenetic Trees
... I think I figured it out! Thanks for your help!!!! ...
written 4 months ago by ResearchR70
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Comment: C: Testing Distances in Phylogenetic Trees
... The tree represents the development of a tumor in comparison to control tissue. The control tissue is derived from two different locations. Now I would like to make a statement if location 1 or location 2 is most likely the ancestor of the tumor. Does this help? ...
written 4 months ago by ResearchR70
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Comment: C: Testing Distances in Phylogenetic Trees
... I already built the tree based in methylation beta-values derived from humans. The bootstrap will create trees based on a random subset of the 'main' tree. Could you please tell me how I can see the common ancestor from that analysis? Btw, thanks for your comment! ...
written 4 months ago by ResearchR70
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Testing Distances in Phylogenetic Trees
... Dear all, I am running a phylogenetic analysis (R-package 'ape') based on methylation data. The samples in my phylogenetic tree can be grouped in three class. Now I would like to test, if group 1 is more similar to group 2 or group 3. Using a bootstrap approach does not really do the job, since I w ...
phylogenetics methylation written 4 months ago by ResearchR70
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Comment: C: Human Brain Cells (450k/EPIC Array)
... Thanks Kevin, I will try it out! ...
written 7 months ago by ResearchR70
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Human Brain Cells (450k/EPIC Array)
... Dear all, I am searching for publicly available methylation profiles of sorted human brain cells (i.e. astrocytes, neurons, oligodendrocytes etc.), done with 450k- or EPIC methylation arrays. I found quite some for other tissue, like breast, but brain seems to be challenging. I would be very thankf ...
450k epic methylation written 8 months ago by ResearchR70
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(Closed) Building Compute Cluster
... Dear Bioinformaticians, I hope this question is correctly placed here and hope that you have a few suggestions for me. A colleague and me would like to build our own computer cluster, but since we do not have funding to hire someone to do so, we have to do this by ourself. 1. Do you have any bo ...
high performance computing compute cluster written 9 months ago by ResearchR70

Latest awards to ResearchR

Popular Question 12 months ago, created a question with more than 1,000 views. For Predicting binding probability of circRNA and miRNA
Scholar 12 months ago, created an answer that has been accepted. For A: Gene Paralogs from GeneCards or Genes Like Me
Popular Question 14 months ago, created a question with more than 1,000 views. For Coordinates for Transcription Start Site (TSS)

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