User: Kristin Muench

gravatar for Kristin Muench
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United States
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kristin_muench
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Email:
k******@stanford.edu

Posts by Kristin Muench

<prev • 129 results • page 1 of 13 • next >
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Comment: C: Seurat on both pooled and unpooled samples
... Hi there! I never got an answer, but I can tell you what I did So - for the initial analysis, I did not attempt to regress out nUMI because I thought over-regressing the data would be the worse sin. However, we were able to find a way to demultiplex the pooled samples that lessened this initial iss ...
written 12 days ago by Kristin Muench470
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Comment: C: SVA Input: Should SVs be calculated on normalized data?
... Great! Thank you very much for your update. ...
written 5 months ago by Kristin Muench470
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Comment: C: miRNAs detected in bulk mRNA-Seq data - how to annotate?
... Thanks for catching that typo, fixed above. I'm wondering that too, whether pri-miRNAs are even a possibility in an mRNA-Seq prep. ...
written 6 months ago by Kristin Muench470
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Comment: C: miRNAs detected in bulk mRNA-Seq data - how to annotate?
... This is a great point. Thank you ...
written 6 months ago by Kristin Muench470
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Comment: C: miRNAs detected in bulk mRNA-Seq data - how to annotate?
... It was not designed to catch miRNAs, thus my confusion. It was a KAPA stranded mRNA-Seq kit: https://www.kapabiosystems.com/product-applications/products/next-generation-sequencing-2/rna-library-preparation-2/kapa-stranded-mrna-seq-kits/ ...
written 6 months ago by Kristin Muench470
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miRNAs detected in bulk mRNA-Seq data - how to annotate?
... Hello, In our bulk mRNA-Seq data, about ~600 of our ~21,000 detected genes were miRNAs. All of these fall within the bounds of expression of non-miRNA genes, and about ~20 miRNAs fall within the upper half of gene expression in the dataset. I was surprised by this because I thought most miRNAs wou ...
R rna-seq mirna written 6 months ago by Kristin Muench470
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Answer: A: Normalizing using Seurat with large numbers of samples
... Update from the future: I did end up running these scripts on a computational cluster using a job scheduler. Once I was able to run these scripts with between 64-128 GB of RAM, I no longer received this issue, and the scripts ran as expected. To run an R script via command line instead of via RStud ...
written 9 months ago by Kristin Muench470
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Answer: A: GATK failing to find any variants - how to troubleshoot?
... Thank you everyone for providing valuable feedback that helped me narrow down the world of what could possibly be going wrong and identifying the key issue. Ultimately, the problem was that I hadn't noticed that at some point the second alignment had failed, and I was trying to run all these comman ...
written 9 months ago by Kristin Muench470
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Comment: C: GATK failing to find any variants - how to troubleshoot?
... Hmm, that's good to know it's unlikely to be the SO:unsorted dict files. Thank you so much for providing feedback on this - tremendously helpful to have a sense for what worked and didn't for other people. ...
written 9 months ago by Kristin Muench470
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Comment: C: GATK failing to find any variants - how to troubleshoot?
... Thank you for taking the time to help with this! This pipeline has been a doozy of a troubleshoot. Regarding $outputDir vs. $idx1Loc: My apologies, these variables both refer to the same path (/resources/KM_GRCh38/star_indices_gatkTutorial_firstPass_STAR_2_7_0d_noGtf) - I ran these in separate scri ...
written 9 months ago by Kristin Muench470

Latest awards to Kristin Muench

Popular Question 5 months ago, created a question with more than 1,000 views. For Which .gtf file should I use when aligning/counting total RNA?
Popular Question 5 months ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Popular Question 5 months ago, created a question with more than 1,000 views. For Determining gene expression with 2 biological replicates and RPKM data only
Popular Question 5 months ago, created a question with more than 1,000 views. For Which .gtf file should I use when aligning/counting total RNA?
Popular Question 5 months ago, created a question with more than 1,000 views. For Which .gtf file should I use when aligning/counting total RNA?
Popular Question 6 months ago, created a question with more than 1,000 views. For Which .gtf file should I use when aligning/counting total RNA?
Popular Question 6 months ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Popular Question 8 months ago, created a question with more than 1,000 views. For Which .gtf file should I use when aligning/counting total RNA?
Popular Question 9 months ago, created a question with more than 1,000 views. For Which .gtf file should I use when aligning/counting total RNA?
Scholar 9 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Scholar 9 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Normal to have high variability in Broad Institute's GSEA Output?
Scholar 10 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Scholar 12 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Popular Question 14 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Scholar 14 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Popular Question 15 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Centurion 15 months ago, created 100 posts.
Popular Question 15 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 16 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 19 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 19 months ago, created a question with more than 1,000 views. For Why can't I replicate DESeq's Log2FC calculation?
Popular Question 21 months ago, created a question with more than 1,000 views. For How many reads should I expect for paired end reads when coverage = 30 million?

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