clusterize
Command clusterize groups together transcripts from different transcriptome assemblies.
usage
$ ingenannot clusterize Gff_transcripts Gff_out
positional arguments:
Gff_transcripts |
Transcripts file in GFF/GTF file |
Gff_out |
Output GFF file with transcripts clusterized per gene |
optional arguments:
-h, –help |
show this help message and exit |
-g,–Gff_genes GFF_GENES |
Gene Annotation file in GFF/GTF file uses to remove transcripts overlapping several CDS |
–keep_atts |
Keep attributes on transcript features |
-r, –overlap_ratio OVERLAP_RATIO |
Overlap ratio between transcripts and CDS from annotations to consider an overlap range[0.0-1.0], default=0.6 |
inputs
Gff transcripts corresponding to a merge of several transcript assembly files with unique identifiers. Ex, transcript files obtained from StringTie with -l option.
outputs
Gff file with transcripts cluterized with the same gene if overlapping.