tetranscripts
Link to section 'Introduction' of 'tetranscripts' Introduction
Tetranscripts is a package for including transposable elements in differential enrichment analysis of sequencing datasets.
For more information, please check its website: https://biocontainers.pro/tools/tetranscripts and its home page on Github.
Link to section 'Versions' of 'tetranscripts' Versions
- 2.2.1
Link to section 'Commands' of 'tetranscripts' Commands
- TEtranscripts
- TEcount
Link to section 'Module' of 'tetranscripts' Module
You can load the modules by:
module load biocontainers
module load tetranscripts
Link to section 'Example job' of 'tetranscripts' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Tetranscripts on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=tetranscripts
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers tetranscripts
TEtranscripts --format BAM --mode multi \
-t treatment_sample1.bam treatment_sample2.bam treatment_sample3.bam \
-c control_sample1.bam control_sample2.bam control_sample3.bam \
--GTF genic-GTF-file \
--GTF genic-GTF-file \
--project sample_nosort_test