filter
ìngenannot filter filters genes based on annotations in gff (TE, …).
usage
$ ingenannot -v 2 filter genes.gff TE.gff genes.noTE.gff -f match -r 0.2
positional arguments:
Gff_genes |
Gene Annotation file in GFF/GTF file format |
Gff_TEs |
Annotation file in GFF/GTF file format |
Output |
Output Annotation file in GFF file format |
optional arguments:
-h, –help |
show this help message and exit |
-s SIZE, –size SIZE |
Minimum required size of feature for filtering, default=300bp |
-f FEATURE, –feature FEATURE |
Feature type expected for filtering, default=match_part |
–bed |
Bed file expected instead of GFF/GTF file |
-r FRACTION, –fraction FRACTION |
Minimum fraction of CDS overlapped for filtering, default=0.1 (10 percent) |
inputs
Gff_genes in GFF/GTF format. GFF_TEs or bed file, with features to take into account to filter the gene file
outputs
Filtered gff file, with only gene structures with gene, mRNA, exon and CDS features. UTRs are removed.