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There may be multiple versions of gffcompare available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail gffcompare

To select a module, type

module load gffcompare/[ver]

where [ver] is the version of choice.

Environment variables set:

On Helix

Sample session:

$ module load gffcompare
[+] Loading gffcompare, version 0.9.8...
$ gffcompare
gffcompare v0.9.8
gffcompare [-r <reference_mrna.gtf> [-R]] [-T] [-V] [-s <seq_path>]
    [-o <outprefix>] [-p <cprefix>] 
    {-i <input_gtf_list> | <input1.gtf> [<input2.gtf> .. <inputN.gtf>]}

 GffCompare provides classification and reference annotation mapping and
 matching statistics for RNA-Seq assemblies (transfrags) or other generic
 GFF/GTF files.
 GffCompare also clusters and tracks transcripts across multiple GFF/GTF
 files (samples), writing matching transcripts (identical intron chains) into
 <outprefix>.tracking, and a GTF file <outprefix>.combined.gtf which 
 contains a nonredundant set of transcripts across all input files (with
 a single representative transfrag chosen for each clique of matching transfrags
 across samples).

 -v display gffcompare version (also --version)
 -i provide a text file with a list of (query) GTF files to process instead
    of expecting them as command line arguments (useful when a large number
    of GTF files should be processed)

 -r reference annotation file (GTF/GFF)

 -R for -r option, consider only the reference transcripts that
    overlap any of the input transfrags (Sn correction)
 -Q for -r option, consider only the input transcripts that
    overlap any of the reference transcripts (Precision correction);
    (Warning: this will discard all "novel" loci!)
 -M discard (ignore) single-exon transfrags and reference transcripts
 -N discard (ignore) single-exon reference transcripts

 -s path to genome sequences (optional); this can be either a multi-FASTA
    file or a directory containing single-fasta files (one for each contig);
    repeats must be soft-masked (lower case) in order to be able to classify
    transfrags as repeats

 -e max. distance (range) allowed from free ends of terminal exons of
    reference transcripts when assessing exon accuracy (100)
 -d max. distance (range) for grouping transcript start sites (100)
 -p the name prefix to use for consensus transcripts in the 
    <outprefix>.combined.gtf file (default: 'TCONS')
 -C discard the "contained" transcripts in the .combined.gtf
    (i.e. collapse intron-redundant transcripts across all query files)
 -E discard "contained" transfrags which are intron compatible with larger
    transfrags (discard intron-redundant transfrags within a query file)
 -F discard intron-redundant transfrags unless they only differ at the 3' end
    and share the 5' end (within the same query file)
 -T do not generate .tmap and .refmap files for each input file
 -V verbose processing mode (also shows GFF parser warnings)
 -D (debug mode) enables -V and generates additional files: 
    <outprefix>.Qdiscarded.lst and <outprefix>.missed_introns.gtf
Interactive job on Biowulf

See the Biowulf user guide for interactive jobs.

Batch job on Biowulf

Create a batch input file following the job submission guide using the example commands on this page.

Swarm of Jobs on Biowulf

Create a swarmfile following the swarm guide using the example commands on this page.