The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF). This program is based on the CuffCompare utility which is part of the Cufflinks/Tuxedo suite, so the various usage options and output files as documented in the CuffCompare manual apply to the gffcompare program as well.

• gffcompare Main Site
• gffcompare on GitHub

• Module Name: gffcompare (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load gffcompare

[user@cn3144 ~]$ gffcompare -R -r mm10.gff -o cuffcmp cufflinks_asm.gtf

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. gffcompare.sh). For example:

#!/bin/bash
set -e
module load gffcompare
gffcompare -R -r mm10.gff -o cuffcmp cufflinks_asm.gtf

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] gffcompare.sh

Create a swarmfile (e.g. gffcompare.swarm). For example:

gffcompare -R -r mm10.gff -o cuffcmp1 cufflinks_asm1.gtf
gffcompare -R -r mm10.gff -o cuffcmp2 cufflinks_asm2.gtf
gffcompare -R -r mm10.gff -o cuffcmp3 cufflinks_asm3.gtf
gffcompare -R -r mm10.gff -o cuffcmp4 cufflinks_asm4.gtf

Submit this job using the swarm command.

swarm -f gffcomapre.swarm [-g #] [-t #] --module gffcompare