TEPID

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Description

Transposable element polymorphism identification. Available is version fixed by Rimjhim Roy Choudhury solving plenty of problems with the original version.

License

GNU GPL v3

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of tepid-fix and load default version of tepid-fix as

module avail tepid-fix/ # list available modules
module load tepid-fix   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail tepid-fix

and choose explicit version you want to use.

Load module tepid-fix (it loads Python 2 modules) and required tools (Bedtools, Bowtie 2, Samblaster, SAMtools and Yaha) and use TEPID:

# Load TEPID
module add tepid-fix
# tepid-map requires bowtie2, samblaster (only for paired-end data), samtools and yaha
module add bowtie2-2.3.0
module add samblaster-0.1.24 # Only for paired-end data
module add samtools-1.9
module add yaha-0.1.83
tepid-map
tepid-map-se
# tepid-discover and tepid-refine require bedtools
module add bedtools-2.26.0
tepid-discover
tepid-refine

Documentation

https://github.com/ListerLab/TEPID/blob/master/README.md and https://github.com/rimjhimroy/TEPID-fix/blob/master/README.md

Homepage

https://github.com/ListerLab/TEPID and https://github.com/rimjhimroy/TEPID-fix