I'm trying to merge 6 gtf files I made with stringtie. I've written their file names in a .txt file in the proper format and named it mergelist.txt. The files I want to merge are in the directory I'm currently using. When I try to run:
stringtie --merge -p 4 -G /home/chris/Desktop/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf -o stringtie_merged.gtf mergelist.txt
I get the error:
Error: cannot find file 'IP1t_stringtie.gtf' and mergelist.txt does not look like GFF!
The IP1t gtf is the first file in the list of 6 gtfs. All appear to be formatted validly if I inspect them, and they're straight out of stringtie itself. I'm sure I'm making a simple mistake, but I can't figure out what it is and googling these errors hasn't turned up anything. Thanks in advance for any help.