# README
TE permutation shuffling analysis.

## Copying some files
```sh
# bubble, or use the graph.gfa
# extract relevant columns and combine 3 columns to get the SV_ID
# cp $HOME/scratch/malawi_transposon/cloud/graph_genome/malawi_haplochromines/malawi_haplochromines-variants3col.bed bubble.bed
# to do: combine the 3 columns to get an sv ID

# chrom sizes

# TE files
ln -s $HOME/scratch/malawi_transposon/cloud/graph_genome/malawi_haplochromines/malawi_haplochromines-variants.bed astCal-variants_raw.bed
ln -s $HOME/scratch/malawi_transposon/cloud/genome/astCal1.2_ensembl/chrom.sizes astCal.chrsizes
ln -s $HOME/scratch/malawi_transposon/cloud/out/repmask/calliptera_repbase_jun21/astCal1.2_ensembl.simple astCal-TE.simple
```

