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Example 3: full workflow without RNAseq one single genome (containing X/Y or two MAT)and no ancestral genome (a.k.a worst case scenario)

1 download example data genome

data needed:

  • genome assembly for haplotype1 containing X/Y or two MAT ( fakegenome.fa.gz in fasta format in the example folder)
  • database of known TE elements (TE.fa.gz in the example folder)
  • txt file with the name of the sex chromosome/MAT and their orientation (scaffold_example3.txt in the example folder)
  • optionally: database of known genes in closely related species (relatedprot.fa.gz in the example folder)

prepare the data

cd example_data
#assemblies and annotation are all deposited on zenodo and available through wget:
wget https://zenodo.org/records/14716941/files/data.tar.gz?download=1
tar zxf data.tar.gz\?download\=1
mv data/* .

in this example we will work with the "fakegenome.fa.gz" it contains two MAT the A1 and A2 with following contig ID: fakegenome_A1 fakegenome_A2

the basename being fakegenome and matching the basename assembly, as expected.

scaffold are provided in the example_folder (named scaffold_example3.txt):

fakegenome fakegenome_A1 N

2 - setting your config file

based on the previous data it is very easy to set up the config file:

option in config description
genome1 ="/path/to/EASYstrata/example_data/fakegenome.fa.gz"
haplotype1 ="fakegenome"
[genome2] =""
[haplotype2] ="fakegenome_A2"
annotate ="YES"
RelatedProt =""
[RNAseqlist] =""
[bamlist1] =""
[bamlist2] =""
[orthoDBspecies] ="Fungi"
fungus ="YES"
TEdatabase ="/path/to/EASYstrata/example_data/TE.fa.gz"
ncbi_species ="fungi"
[gtf1] =""
[gtf2] =""
busco_lineage ="basidyomicota_odb10"
interpro ="NO"
[ancestral_genome] =""
[ancestral_gff] =""
TEancestral =""
scaffolds ="/path/to/EASYstrata/example_data/scaffold_example3.txt"

click here to see the full config file example

3 - creating some files:

use readlink to set full path to text files

4 - launching the workflow :

simply run :

./master.sh -o1 2>&1 |tee log

5 - Results :

the major difference here is that all results plots will be made relatively to the current genome, not to the ancestral genome

this can be a bit problematic to draw accurate inferrence, especially if both haplotype do not recombine.

For the sake of example we provide "fake" data from microbotryum, but beware that the biological results are not necessarily meaningfull:

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