Hi all,

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.