User: jma1991

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jma199130
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Posts by jma1991

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Comment: C: When to combine samples in the pre-processing of 10x scRNA-seq data?
... Thank you Aaron for confirming that empty droplet and doublet detection should be performed separately. However, I'm not sure why you suggested looking at the batch correction workflow? The samples were all prepared on the same chip (albeit in different channels) and sequenced on the same lane of a ...
written 5 months ago by jma199130
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When to combine samples in the pre-processing of 10x scRNA-seq data?
... I am following the Bioconductor [simpleSingleCell][1] workflow for droplet-based data and have a question regarding pre-processing. I have 10x scRNA-seq data from multiple samples. These were prepared in different wells on the same Chromium chip and ran in the same lane of a single flowcell using th ...
scrna-seq 10x written 5 months ago by jma199130 • updated 5 months ago by Aaron Lun25k
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In which order should you detect empty droplets / remove barcode swapping using DropletUtils?
... In which order should you detect empty droplets / remove barcode swapping? The DropletUtils vignette says you should use **all barcodes** for empty droplet detection so I assume this is the first step? Naively I thought that if the amount of barcode swapping was large then the counts for each barcod ...
dropletutils written 6 months ago by jma199130 • updated 6 months ago by s14376430
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Comment: C: Improve limma-voom trend fit to noisy data
... +1 for correcting my misconception, thank you. ...
written 22 months ago by jma199130
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Comment: C: Improve limma-voom trend fit to noisy data
... Apologies, I meant X count in *any* N samples, so not filtering based on any group information. That should be independent of the test statistic. You're right about threshold > strategy. I'd like to automate the pre-filtering stage somehow (picking a decent threshold based on the data, HTSFilter ...
written 22 months ago by jma199130
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Comment: C: Improve limma-voom trend fit to noisy data
... Thanks for the reply Aaron, I've just double-checked on some colleagues computers, the second image should definitely have the highlighted areas ( https://ibb.co/eEkGqG ) I guess the discreteness issue could be improved by filtering based on X values being in N number of replicates (rather than av ...
written 22 months ago by jma199130
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Improve limma-voom trend fit to noisy data
... I'm analysing low cell number ChIP-seq data (3 ChIP replicates / 3 Input replicates). The replicates are highly variable due to the low amount of starting material and the number of PCR cycles used for amplification. I am counting reads into windows along the genome and quantile normalising the coun ...
limma voom written 22 months ago by jma199130 • updated 22 months ago by Aaron Lun25k
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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Sorry, so are you saying OCT4/POU5F1 has transcripts on different chromosomes? ...
written 2.1 years ago by jma199130
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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Actually I'm a bit confused now.. Neither the gene symbol or alias returns the canonical OCT4/POU5F1 gene: library("org.Hs.eg.db") library("TxDb.Hsapiens.UCSC.hg19.knownGene") genes <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene) symbols <- mapIds(org.Hs.eg.db, keys = genes$gene_id, "SYMBOL", k ...
written 2.1 years ago by jma199130
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Answer: A: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... It's called POU5F1B instead of POU5F1: library("TxDb.Hsapiens.UCSC.hg19.knownGene") txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene hg19.genes <- genes(txdb) library("AnnotationDbi") library("org.Hs.eg.db") gene_symbol <- AnnotationDbi::select(org.Hs.eg.db, keys=hg19.genes$gene_id, columns=" ...
written 2.1 years ago by jma199130

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Scholar 2.4 years ago, created an answer that has been accepted. For A: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene

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