Read Me

TEMiner allows to assess the TE compositions of large
quantities of publicly available NGS data.

It first downloads the data with fastq-dump.
Paired end reads will be broken up and concatenated (--split-spot)
Reads are mapped to a database of TE consensus sequences and single copy genes
located on the autosomes: Rhino, rpl32, trafficjam
Than it runs DeviaTE to estimate TE abundance.


Requirements:
- DeviaTE


Sanity check:
Before you start, test the pipeline with a small sample data set

cd scripts  
zsh invasion-history.sh test ../datasets/shorttest.txt

Than check if you get pdfs in the folders results/test/deviate/[tefamily]/
If so, congrats, you are good to go!