User: james.dalgleish

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Posts by james.dalgleish

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Comment: C: two factor chip with diffbind and edgeR (or DESeq2).
... Essentially, you recommend dropping input controls entirely then? ...
written 24 days ago by james.dalgleish20
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Comment: C: two factor chip with diffbind and edgeR (or DESeq2).
... Thanks for the response. Doesn't edgeR expect count data? Wouldn't it be better to provide counts using bedtools subtract using an input control, feed that into a counts matrix, then perform standard edgeR analysis?  Perhaps FC is a valid way to go about it. I'm open to that idea, but it would seem ...
written 24 days ago by james.dalgleish20
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two factor chip with diffbind and edgeR (or DESeq2).
... Is it somehow possible to do a chipseq experiment with two factors (treatment, no treatment), (antibody of interest, control Ig antibody)? I believe that one could do this with edgeR utilizing count data from chipseq and creating a DGEList with the group representing each individual chipseq run, and ...
edger diffbind written 24 days ago by james.dalgleish20 • updated 24 days ago by Aaron Lun18k
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Comment: C: Genomic Features UCSC refseq genes "Download the knownGene table ... Error: Bad
... Is there a working github repo I can use to install it with devtools::install.github()? ...
written 4 weeks ago by james.dalgleish20
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Comment: C: Genomic Features UCSC refseq genes "Download the knownGene table ... Error: Bad
... I still can't seem to quite download it yet using install.packages() and the rtracklayer page (https://bioconductor.org/packages/release/bioc/html/rtracklayer.html) doesn't reflect the new version. Let me know if there is a way to access it otherwise.   ...
written 4 weeks ago by james.dalgleish20
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Genomic Features UCSC refseq genes "Download the knownGene table ... Error: Bad Request"
... Hello,   I'm attempting to use refseq genes for plotting with Gviz and I am having trouble creating a txdb from UCSC to begin the process, but I'm getting an error: > library(GenomicFeatures) > hg19.refseq.db<-makeTxDbFromUCSC(genome="hg19", table="refGene") Download the refGene table .. ...
genomicfeatures written 4 weeks ago by james.dalgleish20 • updated 4 weeks ago by Michael Lawrence9.9k
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seqlevels(param) not in BAM header
... ------------------------------------------------------------ Info: setting summary ------------------------------------------------------------ Name of aligned read file: SRR3105506.sorted.filtered.bam Aligned read file format: BAM Directory of processed bin-level files: ./jmosaics/ Construct bin-le ...
jmosaics written 6 weeks ago by james.dalgleish20
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Answer: A: TxDb errors in GenomicFeatures package-- cannot load TxDb with standard params f
... It turns out it's an rtracklayer bug. I received the following response on the GenomicFeatures github site: Hi @jamesdalg, Thanks for the report. The error is actually happening in the rtracklayer package. It's easy to reproduce with: library(rtracklayer) session <- browserSession() genome(se ...
written 11 weeks ago by james.dalgleish20
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possible Rtracklayer issue: TxDb errors in GenomicFeatures package-- cannot load TxDb with standard params from UCSC (issue began last night)
... I've been running code that used this for a long time and it just started breaking last night. Another colleague also is having issues on version 31 of GenomicFeatures. > hg19.refseq.db<-GenomicFeatures::makeTxDbFromUCSC(genome="hg19", table="refGene") Error in names(trackIds) <- sub("^ ", ...
rtracklayer genomicfeatures txdb maketxdbfromucsc maketxdbfrombiomart written 11 weeks ago by james.dalgleish20 • updated 10 weeks ago by Michael Lawrence9.9k

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