User: dsull

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dsull1.6k
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Name: Delaney Sullivan

Currently at UCLA (formerly at Stanford)

Posts by dsull

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Comment: C: Does anyone know/would be willing to give me a guide on how to do ChIP-Seq data
... I'd recommend looking at the methods section of published papers. Many good papers will present reproducible code or in-depth description of pipelines on how to reproduce their ChIP-Seq analysis. ...
written 5 days ago by dsull1.6k
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Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
... Well, you can only work with what you have. You can basically only characterize the abundance of the genes you have relative to one another; if there happens to be an unannotated/unmapped gene not expressed at all in sample #1 but constitutes the majority of the reads in sample #2, your between-samp ...
written 6 days ago by dsull1.6k
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Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
... I don't see how you can be unsure of the RPKM; you take the number of reads mapped to a transcript, divide by its length (in kilobases), and divide by the total number of mapped reads. There's really no other way to be sure vs. unsure unless you misapply the mathematical formula. Sum of TPMs will ...
written 6 days ago by dsull1.6k
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Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
... TPM *is* "relative abundance". A TPM of 158783.9 is not incorrect and it's not overboard -- it means that that transcript's abundance is high (relative to the other mapped transcripts). Consider this hypothetical situation: If all of your reads mapped to two transcripts, one of those transcripts i ...
written 6 days ago by dsull1.6k
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Answer: C: [RNA-Seq] STAR vs Subread
... To answer the question "Is there any reason why we still use TPM for downstream analysis? and when do we need to use TPM?", there are plenty of reasons to use TPM in downstream analysis. Differential gene expression is only one type of downstream analysis. There are others: GSEA, correlation between ...
written 6 days ago by dsull1.6k
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Comment: C: correct order for pathway analysis
... I agree with what JC said. Additionally, I recommend using an updated, well-maintained pathway tool such as enrichr: https://maayanlab.cloud/Enrichr/ instead of DAVID. ...
written 26 days ago by dsull1.6k
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Comment: C: Batch effects vs biological variables
... I'd be wary when doing batch correction while informing the batch correction tool about your biological conditions. Try permuting your condition (metastasis/control) labels and see how the clustering looks following ComBat. I personally only do ComBat-type stuff when I don't deal with biological co ...
written 5 weeks ago by dsull1.6k
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Comment: C: Kallisto missing Bootstrap
... You cannot use your current kallisto installation to get the abundance.h5 files containing the bootstraps. You have to re-install kallisto (see my previous comment). ...
written 6 weeks ago by dsull1.6k
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Comment: C: Kallisto missing Bootstrap
... Download the binaries rather than compiling from source. If you do want to build it from source, be sure to specify`-DUSE_HDF5=ON` when running cmake. ...
written 6 weeks ago by dsull1.6k
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Comment: C: Any other way to validate RNA-seq data if qPCR tests is not available?
... Relevant twitter thread: https://twitter.com/andy_utoronto/status/1266144011259195394 ...
written 7 weeks ago by dsull1.6k

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