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