stringtie step, I estimated transcript abundances and created table counts for
In a folder "ballgown", I have the all the sample subdirectories inside this folder "ballgown". Each sample subdirectory have following files:
e2t.ctab e_data.ctab i2t.ctab i_data.ctab TCGA-XX-XXX-XX_GRCh38.gtf t_data.ctab
To get the FPKM matrix I did like below:
library(ballgown) my.data <- ballgown(dataDir = "ballgown", samplePattern = "TCGA", meas="all") Sun Aug 25 14:12:19 2018 Sun Aug 25 14:12:19 2018: Reading linking tables Sun Aug 25 14:12:29 2018: Reading intron data files Sun Aug 25 15:00:38 2018: Merging intron data Killed !
I tried couple of times but I got the same error. What could be wrong here? Did I do something wrong?