tophat
Link to section 'Description' of 'tophat' Description
Spliced read mapper for RNA-Seq.
Link to section 'Versions' of 'tophat' Versions
- Anvil: 2.1.2
Link to section 'Commands' of 'tophat' Commands
- bam2fastx
- bam_merge
- bed_to_juncs
- contig_to_chr_coords
- fix_map_ordering
- gtf_juncs
- gtf_to_fasta
- juncs_db
- long_spanning_reads
- map2gtf
- prep_reads
- sam_juncs
- samtools_0.1.18
- segment_juncs
- sra_to_solid
- tophat
- tophat2
- tophat-fusion-post
- tophat_reports
Link to section 'Module' of 'tophat' Module
You can load the modules by:
module load tophat
Link to section 'Example job' of 'tophat' Example job
To run TopHat on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=tophat
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module load tophat
tophat -r 20 test_ref reads_1.fq reads_2.fq