https://github.com/lkremer/tecov

A pipeline to to determine the repeat content of genes and their neighboring regions.
https://github.com/lkremer/tecov

bioinformatics-pipeline genome genomics repeatmasker transposable-elements

Last synced: 5 months ago
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A pipeline to to determine the repeat content of genes and their neighboring regions.

• Host: GitHub
• URL: https://github.com/lkremer/tecov
• Owner: LKremer
• License: mit
• Created: 2017-06-02T13:24:35.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2017-06-02T13:25:14.000Z (over 8 years ago)
• Last Synced: 2025-03-31T21:27:58.204Z (7 months ago)
• Topics: bioinformatics-pipeline, genome, genomics, repeatmasker, transposable-elements
• Language: Python
• Size: 6.84 KB
• Stars: 7
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
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](http://www.repeatmasker.org/)

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+](https://www.python.org/downloads/) and the Python package pyfaidx:

`pip3 install pyfaidx`

You also need to [install bedtools](http://bedtools.readthedocs.io/en/latest/content/installation.html).

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")

```