I need help with the ballgown analysis (which I intent to use for my RNA-seq data with 3 replicates).
Right now, I am practising myself with this new tools by using the data provided in the article "Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown". Everything went fine till Stringtie.
I am new to R program, I tried to do every step as mention but I encountered a problem when reading the input files. Can anyone help me with the problem.
The commands I used in the R program are as follows:
>library(ballgown) >library(RSkittleBrewer) >library(genefilter) >library(dplyr) >library(devtools) >pheno_data = read.csv("geuvadis_phenodata.csv") >bg_chrX = ballgown(dataDir = "ballgown", samplePattern = "ERR", pData=pheno_data) <------------------ This is the place where I get error
Error Message as follows:
Tue May 8 11:37:10 2018 Tue May 8 11:37:10 2018: Reading linking tables Tue May 8 11:37:10 2018: Reading intron data files Error in read.table(file, header = TRUE, sep = "\t", colClasses = cc, : no lines available in input
When I tired to traceback the problem with traceback() command, I get the following output which makes no sense to me
4: stop("no lines available in input") 3: read.table(file, header = TRUE, sep = "\t", colClasses = cc, quote = "") 2: .readIntron(f, meas) 1: ballgown(dataDir = "ballgown", samplePattern = "ERR", pData = pheno_data)
I am not sure what is the problem with my method. Can anyone help me with this issue? Only if I can solve this, I can use this pipeline to analysis my RNA-seq time course data with 3 replicates.
Thanks in advance.