TEsn

Snakemake version of the TEs identification and genotyping pipeline.

Inputs:

• File with sites genomic coordinates.
  cat probeLocationFile_v8.txt | awk '{print $1}' | sed 's/..$//' > sites_list

mkdir -p sites_files
awk -F" " '{print ($1 FS $1)}' sites_list | sed 's/:.* / /' | awk  -F" " '{print $2 >"sites_files/"$1}'

Create yaml for conda env: conda env export > env.yaml

Run snakemake

snakemake -c1 --use-conda
snakemake --jobs 100 \
          --cluster "sbatch \
          -J sn1 \
          -A DURBIN-SL2-CPU \
          -p cclake \
          --time 29:00:00" \
          --use-conda &

Fields of alldatamerge: ref start end total_reads m_reads clips_r clips_l consensus_l consensus_r

snakemake --use-conda -c1