User: Kristin Muench

gravatar for Kristin Muench
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kristin_muench
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Posts by Kristin Muench

<prev • 130 results • page 1 of 13 • next >
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Why don't we apply multiple hypothesis testing correction for multiple bouts of differential expression analysis?
... Hello all, I've seen people recommend repeating DESeq analysis if you want to do study multiple contrasts for a single factor, for example: https://www.biostars.org/p/325009/#325036 However, in the above, aren't you rerunning hypothesis tests repeatedly? Why isn't there an additional step of p-val ...
rna-seq written 7 weeks ago by Kristin Muench540
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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 months ago by Kristin Muench540
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Comment: C: SVA Input: Should SVs be calculated on normalized data?
... Great! Thank you very much for your update. ...
written 17 months ago by Kristin Muench540
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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 19 months ago by Kristin Muench540
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Comment: C: miRNAs detected in bulk mRNA-Seq data - how to annotate?
... This is a great point. Thank you ...
written 19 months ago by Kristin Muench540
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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 19 months ago by Kristin Muench540
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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 19 months ago by Kristin Muench540
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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 21 months ago by Kristin Muench540
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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 22 months ago by Kristin Muench540
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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 22 months ago by Kristin Muench540

Latest awards to Kristin Muench

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?
Student 6 months ago, asked a question with at least 3 up-votes. For Should kallisto take hours to run?
Popular Question 6 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 6 months ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Normal to have high variability in Broad Institute's GSEA Output?
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 7 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 12 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 12 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 12 months ago, created a question with more than 1,000 views. For Could a "complete" RNA-Seq database feasibly exclude some protein-coding transcripts?
Popular Question 12 months ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Popular Question 17 months ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Popular Question 17 months ago, created a question with more than 1,000 views. For Could a "complete" RNA-Seq database feasibly exclude some protein-coding transcripts?
Popular Question 17 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 17 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 17 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 18 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 19 months ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Popular Question 19 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 20 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 21 months ago, created a question with more than 1,000 views. For Which .gtf file should I use when aligning/counting total RNA?
Scholar 21 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2

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