Inputs

• genome fasta for the organism of interest
• TE fasta for the TE consensus
• a bigbed file used for annotation of the TE consensus hub
• a config file where the user designates which parameters to use

Outputs

• summary files containing genomic coordinates of each region of the genome that is aligned with a TE
• summary files containing the total regions of the genome and total nucleotides that correspond to full TE and to partial TE fragments
• a fasta file of every complete TE that was found in the genome
• a folder of files that enable visualization of the results in the ucsc genome browser

Dependencies

• a conda environment with snakemake installed (instructions for installing at link below)

  https://snakemake.readthedocs.io/en/stable/getting_started/installation.html

Using the Pipeline

• open the summarize_TE_config.yaml file edit the parameters there
• open terminal and cd into the folder that has the summarize_TE.smk file
• activate the conda snakemake environment and run the command below snakemake -s summarize_TE.smk --use-conda --cores 4

Uploading to ucsc broswer

• open the folder you created while using the pipeline and locate the ucsc_browser folder
• copy the entire ucsc_broswer folder into the public folder where your ucsc broser files are stored
• Visit the ucsc genome browser website
• click on "My Data" then "Connected Hubs"
• add urls pointing to the assembly hub, the track hub, and the annotation hub from the ucsc browser folder you just copied

Important note about annotation file

• we created a bigbed annotation file from the dfam embl file that can be imported to the ucsc browser
• the bigbed coordinates were altered to match each TE instead of the entire genome
• this annotation hub provides another track in the ucsc viewer that shows internal regions and LTRs and any annotated protein encoding genes

multiple summaries

if a collection of genomes has been assembled in a single directory this pipeline can analyze all of them at once

• output is a collection of summaries of the total regions, etc for each genome
• combined summary is all of the genomes combined into one file with a single number to represent the presence of each transposon
  • I'd like to have this number be equal to the total number of matching nucleotides divided by the total number of nucleotides present in the total regions if every region was a full copy