Hello, I am facing an error while loading my data structure in ballgown tool, I have tried following are the commands which i am using in my data:
>setwd("/Users/kchougul/data/testdata/Ballgown/tutorial_example") >library(ballgown) >library(ggplot2) >library(gplots) >library(genefilter) >library(GenomicRanges) >library(plyr) >pheno_data = read.csv(file ="design_matrix", header = TRUE, sep = ",") >sample_full_path <- paste("SRRXXX", "SRRYYY", "SRRZZZ",pheno_data[,1], sep = ',')
SRRYYY are my ballgown folders containing respective
>bg = ballgown(samples=as.vector(sample_full_path),pData=pheno_data) Tue Nov 13 13:13:27 2018 Error in ballgown(samples = as.vector(sample_full_path), pData = pheno_data) : Something is wrong: are you missing .ctab files? Do extra files/folders (other than tablemaker output folders) match your samples/dataDir/samplePattern argument(s)?
You should report this as a bug on GitHub site. That is the official place to repport bugs.
But why do you want to use ballgown? Which tool have you used to quantify the RNASeq data?
Thanks for your reply.
I have used StringTie for quantification
Thank you very much, @kristoffer.vittingseerup and @ATpoint. I appreciate your help.