I’m having problems merging the GTF files generated with Stringtie. I know it must me a simple mistake that I m doing with the cmdline but also googling I couldn’t figure it out.
The command line that I’m using for merging the files is this:
stringtie --merge -G Homo_sapiens.GRCh37.75.gtf -p 8 -o Treated_1.gtf Treated_2.gtf Treated_3.gtf Untreated_1.gtf Untreated_2.gtf Untreated_3.gtf gtf_list.txt Error: no transcripts were found in input file gtf_list.txt
Beside the error that , it generates a folder with files inside named “Transcript_s000.bam and sam” but I can’t understand why it stops working.
In the file "gtf_list.txt' I listed the file name_gtf
Can you please help me with that?