TE TRANSFER

Programs versions used:

• BEDTools/2.27.1-foss-2018b
• minimap2/2.11-foss-2016b
• Python/3.7.2-GCCcore-8.2.0

Step to follow to transfer TEs and genes:

Set varaible names

• wdir = working directory
• strain = base name of a strain (i.e., STO-022)
• FastaPath = full path to fasta file of genome assemble
• TEAnnotation = full path to TE annotation file in bed format
• RefrencePath = full path to Reference genome in fasta format
• genes2strain = sam file transfer of genes from reference genomes to strains
• cds2strain = sam file transfer of cds from reference genomes to strains
• githubData = full path to the data folder inside this repository

Prepare CDS and genes reference fasta

Download the following files from flyBase and change accordingly in the following script:

• dmel-all-r(VERSION).gtf'
• dmel-all-gene-r(VERSION).fasta
• dmel-all-CDS-r(VERSION).fasta

python cds_gene_fasta_preparation.py wdir

TE fasta sequence

$ python bedTE2Fasta.py wdir strain TEAnnotation FastaPath

Nested and tandem TEs

$ python nested_tandem_TE_classification.py wdir strain TEAnnotation

Gene transfer

Run Minimap2 in splice-aware mode, and without it (Reference_genes.fasta and Reference_primary_cds.fasta: produced by cds_gene_fasta_preparation.py)

$ python gene_transfer.py wdir strain FastaPath

TE transfer

$ python TE_transfer.py wdir strain RefrencePath TEAnnotation githubData