gffcompare

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.