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TEcov, a pipeline to to determine the repeat content of genes and their neighboring regions.

Requires a gene annotation in ".gff" format and a RepeatMasker repeat annotation in ".out" format. Reports the repeat content (% of base pairs covered) of

  • genic regions (exons, introns, untranslated regions)
  • promoter regions (upstream regions)
  • flanking regions (up- and downstream regions)

The results can be used to study the influence of repetetive content such as transposable elements (TEs) on gene expression or gene family evolution.

Requirements

TEcov requires Python3.4+ and the Python package pyfaidx:

pip3 install pyfaidx

You also need to install bedtools.

Usage

usage: TEcov.py [-h] [-f FLANK_SIZE] [-j JOBNAME] [-m MIN_BASEPAIRS]
                [--gene_gff_feat GENE_GFF_FEAT] [--cds_gff_feat CDS_GFF_FEAT]
                species_gff te_annotation genome

A pipeline to determine the repeat content (e.g. content of transposable
elements) of genes and their neighboring regions. Requires a gene annotation
and a repeatmasker repeat annotation. Reports the repeat content (%bp covered)
of genic regions (exons, introns, UTRs), promoter (upstream) regions and
flanking (up- and downstream) regions.

positional arguments:
  species_gff           path to the species' genome annotation (.gff, only
                        longest isoforms!)
  te_annotation         path to the species' TE annotation (repeatmasker .out
                        but NOT .gff)
  genome                path to the species' genome (.fasta).

optional arguments:
  -h, --help            show this help message and exit
  -f FLANK_SIZE, --flank_size FLANK_SIZE
                        how long the flanking regions should be (in bp,
                        default is 10.000 bp)
  -j JOBNAME, --jobname JOBNAME
                        name a directory to which all intermediate files will
                        be dumped
  -m MIN_BASEPAIRS, --min_basepairs MIN_BASEPAIRS
                        percentages get meaningless when the overlapped
                        sequences are very short. This value defines the
                        minimun sequence length (in bp). Shorter sequences
                        will be "NA" (default: 200 bp)
  --gene_gff_feat GENE_GFF_FEAT
                        the name of the GFF feature that denotes the location
                        of genes (default: "gene")
  --cds_gff_feat CDS_GFF_FEAT
                        the name of the GFF feature that denotes the location
                        of CDSs (default: "cds")