User: Kristin Muench

gravatar for Kristin Muench
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kristin_muench
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5 years ago
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k******@stanford.edu

Posts by Kristin Muench

<prev • 128 results • page 1 of 13 • next >
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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 days ago by Kristin Muench450
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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 7 weeks ago by Kristin Muench450
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Comment: C: miRNAs detected in bulk mRNA-Seq data - how to annotate?
... This is a great point. Thank you ...
written 7 weeks ago by Kristin Muench450
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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 7 weeks ago by Kristin Muench450
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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 7 weeks ago by Kristin Muench450
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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 4 months ago by Kristin Muench450
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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 4 months ago by Kristin Muench450
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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 4 months ago by Kristin Muench450
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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 4 months ago by Kristin Muench450
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Comment: C: GATK failing to find any variants - how to troubleshoot?
... Yeah, I just tried it again and there is no "SO" flag in the .dict file I produced using the code I posted above: @HD VN:1.6 @SQ SN:10 LN:133797422 M5:907112d17fcb73bcab1ed1c72b97ce68 UR:file:/resources/KM_GRCh38/sequence/GRCh38_r95.all.fa @SQ SN:11 LN:135086622 ...
written 4 months ago by Kristin Muench450

Latest awards to Kristin Muench

Popular Question 17 days ago, created a question with more than 1,000 views. For Which .gtf file should I use when aligning/counting total RNA?
Popular Question 25 days 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 weeks 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 weeks ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Popular Question 3 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 4 months ago, created a question with more than 1,000 views. For Which .gtf file should I use when aligning/counting total RNA?
Scholar 4 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Scholar 4 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Teacher 5 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 5 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Scholar 7 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Popular Question 9 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Scholar 9 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Popular Question 10 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Centurion 10 months ago, created 100 posts.
Popular Question 10 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 11 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
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?
Popular Question 14 months ago, created a question with more than 1,000 views. For Why can't I replicate DESeq's Log2FC calculation?
Popular Question 16 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?
Great Question 18 months ago, created a question with more than 5,000 views. For Bowtie2: Why won't it recognize my index files?
Supporter 18 months ago, voted at least 25 times.
Popular Question 2.1 years 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?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?

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