User: Kristin Muench
Kristin Muench • 470
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- kristin_muench
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- Joined:
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- k******@stanford.edu
Posts by Kristin Muench
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... 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 Muench • 470
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... Great! Thank you very much for your update. ...
written 5 months ago by
Kristin Muench • 470
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... 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 Muench • 470
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... This is a great point. Thank you ...
written 6 months ago by
Kristin Muench • 470
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... 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 Muench • 470
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... 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 ...
written 6 months ago by
Kristin Muench • 470
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... 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 Muench • 470
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... 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 Muench • 470
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... 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 Muench • 470
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... 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 Muench • 470
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