Hello,

I have followed an RNA-seq analysis in galaxy and with the resulting SQLite database, I am trying to generate figures. After I loaded my SQlite data from galaxy into the working directory I set for R, I used the following trunk of codes in R (R-3.4.4);

source("https://bioconductor.org/biocLite.R")
biocLite("cummeRbund")
library(cummeRbund)
directory <- ("./specdata/")
cuff_data <- readCufflinks ("C:/Users/dkilic/Desktop/Using_R/Analyse_RNA_seq_data_from_public_repository/Manually_downloaded_SRA_files/data_from_galaxy")

cuff_data

and I got this;

CuffSet instance with:

0 samples

0 genes

0 isoforms

0 TSS

0 CDS

0 promoters

0 splicing

0 relCDS

Name of my sqlite file is "mycobacterium_macrophage_infection". What do you think is the problem?