Single locus resolution of Transposable ELEment expression. Telescope estimates transposable element expression (retrotranscriptome) resolved to specific genomic locations. It directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model.

References:

• Matthew L Bendall, Miguel de Mulder, Luis Pedro Iñiguez, Aarón Lecanda-Sánchez, Marcos Pérez-Losada, Mario A Ostrowski, Richard B Jones, Lubbertus Mulder, Gustavo Reyes-Terán, Keith A Crandall, Christopher E Ormsby, Douglas F. Nixon. Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. bioRxiv 398172; doi: 10.1101/398172

• Telescope Main Site

• Module Name: telescope (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load telescope
[+] Loading telescope, version 1.0.2... 
[user@cn3144 ~]$ telescope assign [samfile] [gtffile]
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. telescope.sh). For example:

#!/bin/bash
set -e
module load telescope
telescope assign [samfile] [gtffile]

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] telescope.sh

Create a swarmfile (e.g. telescope.swarm). For example:

telescope assign [samfile1] [gtffile]
telescope assign [samfile2] [gtffile]
telescope assign [samfile3] [gtffile]
telescope assign [samfile4] [gtffile]

Submit this job using the swarm command.

swarm -f telescope.swarm [-g #] [-t #] --module telescope