TEBAG

Transposable Elements By Age Group

To Do's and Notes

2022_07_07

• Finish drafting liftover
• Intersection code -- python or R?
• Input: names, abundance, DESeq
• VCF: think about
• Test: LTR7up paper for comparison
  • link to test bed
  • take this, use to filter our bed, use as test
• Paper: re-process some data, demonstrate performance
• Undergrads: how to get involved

sample run command

nextflow run main.nf --generate_db --species_paths bin/sample_generate_csv.csv --human_bed ../beds/ucsc.rmsk.salmon.bed -with-docker ubuntu:18.04 -resume