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 or BAM 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