data needed:
- genome assembly for Silene latifolia
- RNAseq data from Silene latifolia
- database of known TE elements
- txt file with the name of the ancestral sex chromosome and their orientation
- optionally: database of known genes in closely related species
S. latifolia genome assembly is available on NCBI at the following link: insert_link_here
RNAseq data are available at XXXXX and can be download from there
a set of TE for plant can be obtained here:
for plants:
wget https://trep-db.uzh.ch/downloads/trep-db_nr_Rel-19.fasta.gz
then this should be added to the config file
note that repeatexplorer could also work
download with:
wget http://repeatexplorer.org/repeatexplorer/wp-content/uploads/Viridiplantae_v3.0_ALL_protein-domains_repet_formated.fa
| option in config | description |
|---|---|
| genome1 | ="/path/to/EASYstrata/example_data/Slatifolia.fa.gz" |
| haplotype1 | ="Slatifolia" |
| [haplotype2] | ="Slatifolia_Y" |
| annotate | ="YES" |
| RelatedProt | ="/path/to/EASYstrata/example_data/relatedprot.fa.gz" |
| [RNAseqlist] | ="/path/to/EASYstrata/example_data/rnaseq.list.example5.txt" |
| [orthoDBspecies] | ="Viridiplantae" |
| fungus | ="NO" |
| TEdatabase | ="/path/to/EASYstrata/example_data/trep-db_nr_Rel-19.fasta.gz" |
| ncbi_species | ="eudicots" |
| busco_lineage | ="viridiplantae_odb10" |
| interpro | ="NO" |
| scaffolds | ="//path/to/EASYstrata/example_data/scaffold_example5.txt" |
click here to see the example
3 - launching the workflow :
./master.sh -o1 2>&1 |tee log
4 - results visualisation :
see example1 to see examples plots