Hi According to this protocol
I have generated the gtf files for ballgown but now i want to use the Deseq. for the Deseq tool i have to generate the text file of gene and transcripts files. I have run the python script for one samples as
python prepDE.py ./ballgown/sample1/sample1.gtf
I gave me 2 output files. I run this command for one sample. My number of samples is 3. Can i have to run the same command for other 2 samples?