User: supremerulersuraj

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Posts by supremerulersuraj

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Comment: C: Handling pseudogenes in RNA-seq
... Thanks for the response. That's true, but I was hoping there might be some bioconductor solution for coalescing pseudogenes to their corresponding canonical gene post-mapping (i.e. with the counts table). I didn't know if anybody had experience with doing this. I included the mapping information jus ...
written 5 months ago by supremerulersuraj0
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Handling pseudogenes in RNA-seq
... I recently performed an RNA-seq experiment that was mapped using STAR through a package called zUMIs. Typically, our reads are 66 bp (and in the past our experiments have been mapped to the human genome) but this time our data ended up being 50 bp reads to the mouse genome. Our final counts dataset ...
counts star rna-seq pseudogenes written 5 months ago by supremerulersuraj0 • updated 5 months ago by Levi Waldron790
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Converting scater-normalized UMI data to Monocle CellDataSet
... I had a question regarding the appropriate distribution for modeling scater-normalized UMI data. I normalized the UMI dataset (a SingleCellExperiment) to the ERCC spike-ins to capture total differences in RNA content. I then used the convertTo() function in scran to export to Monocle CellDataSet so ...
monocle scran scater umi written 6 months ago by supremerulersuraj0 • updated 6 months ago by Aaron Lun21k
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Answer: A: Normalizing to multiple spike-in concentrations with scran
... Thanks for the explanation. We luckily have cells from the same biological group in another batch that received the 1x spike-in. When looking at PCA/t-SNE, they cluster by biological group rather than batch, which is promising, but we will definitely do batch correction as you suggested to be sure. ...
written 6 months ago by supremerulersuraj0
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Normalizing to multiple spike-in concentrations with scran
... I have a single cell RNA-seq dataset acquired using a UMI protocol with ERCC spike-ins. I would like to normalize to spike-ins (to be able to maintain information about endogenous differences in mRNA). I was planning to do this in scran through computeSpikeFactors. However, it happened during sample ...
scran spike-in written 7 months ago by supremerulersuraj0
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Comment: C: Handling outliers in DESeq2?
... Thanks for the tip on plotCounts()! This sample is not consistently an outlier. It seems most probable that that value is technical error/noise as opposed to real signal. I understand that n = 4, 5 is small, but for the sake of my understanding, is there a reason why replaceOutliersWithTrimmedMeans ...
written 18 months ago by supremerulersuraj0
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Handling outliers in DESeq2?
... I am currently using DESeq2 to analyze differential expression in some bulk RNA-seq samples, and am running into an issue that I assume is an outlier issue? I essentially have two groups with two conditions (in vitro and invivo, tbx and hcn). I perform DESeq analyses on the in vitro and in vivo samp ...
deseq2 sample outliers written 18 months ago by supremerulersuraj0 • updated 18 months ago by Michael Love20k

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