User: Kristin Muench

gravatar for Kristin Muench
Reputation:
500
Status:
Trusted
Location:
United States
Twitter:
kristin_muench
Last seen:
1 day, 16 hours ago
Joined:
5 years, 10 months ago
Email:
k******@stanford.edu

Posts by Kristin Muench

<prev • 129 results • page 1 of 13 • next >
0
votes
0
answers
554
views
0
answers
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 6 months ago by Kristin Muench500
0
votes
0
answers
1.1k
views
0
answers
Comment: C: SVA Input: Should SVs be calculated on normalized data?
... Great! Thank you very much for your update. ...
written 11 months ago by Kristin Muench500
0
votes
1
answer
355
views
1
answers
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 12 months ago by Kristin Muench500
0
votes
1
answer
355
views
1
answers
Comment: C: miRNAs detected in bulk mRNA-Seq data - how to annotate?
... This is a great point. Thank you ...
written 12 months ago by Kristin Muench500
0
votes
1
answer
355
views
1
answers
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 12 months ago by Kristin Muench500
6
votes
1
answer
355
views
5 follow
1
answer
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 12 months ago by Kristin Muench500
1
vote
1
answer
1.2k
views
1
answers
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 15 months ago by Kristin Muench500
1
vote
1
answer
842
views
1
answers
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 15 months ago by Kristin Muench500
0
votes
1
answer
842
views
1
answers
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 15 months ago by Kristin Muench500
0
votes
1
answer
842
views
1
answers
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 15 months ago by Kristin Muench500

Latest awards to Kristin Muench

Popular Question 7 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 27 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 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 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 11 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 11 months ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Popular Question 11 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 11 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 11 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 11 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 How to make lumi accept .txt data?
Popular Question 14 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 15 months ago, created a question with more than 1,000 views. For Which .gtf file should I use when aligning/counting total RNA?
Scholar 15 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Scholar 15 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Teacher 16 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 16 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Scholar 17 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Popular Question 20 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Scholar 20 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Popular Question 20 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1643 users visited in the last hour