User: warrena
warrena • 0
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Posts by warrena
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... I am trying to get mm10 gene annotations with gene names. I have tried the following:
ncbiRefSeq = makeTxDbFromUCSC(genome="mm10", tablename="ncbiRefSeq")
geneid = makeTxDbFromUCSC(genome="mm10", tablename="geneid")
knownGene = makeTxDbFromUCSC(genome="mm10", tablename="knownGene")
In the first ...
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Comment:
C: error with detectTranscripts
... Thanks, Anusha. This worked. I'll add that for users of R 3.4.4 I had to call keepStandardChromosomes() with pruning.mode="coarse". Here is the code:
require(groHMM)
library(IRanges)
library(GenomicRanges)
library(Rsamtools)
library(GenomicAlignments)
data <- readGAlignments("poolA_index1_samp ...
written 4 months ago by
warrena • 0
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... Greetings,
I am attempting to use detectTranscripts() from groHMM using bams from a PRO-seq experiment. I am getting the following error:
Error in Fp[[i]] + 1 : non-numeric argument to binary operator
In addition: Warning messages:
1: In mclapply(readsList, function(x) { :
all scheduled cores en ...
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... I have PRO-seq data with the following conditions: untreated (time 0), vehicle, and treatment (3 replicates each, 4 time points for each vehicle/treatment combination). I would like to evaluate treatment effects as a function of time. I have done the following:
1. Divided the reads in each conditio ...
written 4 months ago by
warrena • 0
• updated 4 months ago by
Michael Love ♦ 20k
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