Telescope - mlbendall/telescope_tutorial GitHub Wiki
Input
Telescope requires two key inputs for TE quantification:
- Gene model representing transposable element transcripts. This should be in GTF format.
- Alignment of reads to the reference genome. This should be in
SAM
orBAM
format and not coordinate sorted. (Telescope expects all possible alignments for a read to appear consecutively in the file)
I have created several annotations that are compatible with Telescope, available here.
For this tutorial we will download the HERV annotation for hg38:
wget -O HERV_rmsk.hg38.gtf https://github.com/mlbendall/telescope_annotation_db/raw/master/builds/HERV_rmsk.hg38.v2/transcripts.gtf