Where:
Run gffcompare in the same folder as your gtf files. When
stringtie-merge completes, you should already have a blreads
window in the gtffiles folder.
Input:
No files need to be selected before opening this menu.
Reference transcriptome (.gtf) - This is the transcriptome
(set of mRNAs) corresponding to the genes in the genome. The file
should probably be in the same directory as the genome file.
Merged
transcriptome (.gff/.gtf) - This is the file created by stringtie-merge eg. merged.gtf.
Name prefix - This will be added to the name of every gene
transcript in the output, so it should be short. For example, a
descriptive prefix for transcripts from Rhodosporidium
diobovatum, might be Rdio.
Output:
Several files with the Name prefix will be written to the
current folder. A summary can be
found in the .stats file (eg. merged.stats). This file
should also pop up in a text editor.
For more
information on the other files, see the Gffcompare
User's Guide.