tailseeker on Biowulf
Tailseeker is the official pipeline for TAIL-seq, which measures poly(A) tail lengths and 3′-end modifications with Illumina SBS sequencers.
References:
- Chang, Hyeshik et al. TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications. Molecular Cell. 53 (6) 1044 - 1052. doi:10.1016/j.molcel.2014.02.007
Documentation
Important Notes
- Module Name: tailseeker (see the modules page for more information)
- Reference data in /fdb/tailseeker/
- Before running tailseeker, you must generate a run configuration tailseeker.yaml file from http://hyeshik.github.io/tailseeker/generate-settings.html and place that file in the directory from which you call tseek.
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive --cpus-per-task 8 --mem 32g 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 tailseeker [user@cn3144 ~]$ tseek -j $SLURM_CPUS_PER_TASK [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. tailseeker.sh). For example:
#!/bin/bash set -e module load tailseeker test -n "$SLURM_CPUS_PER_TASK" || SLURM_CPUS_PER_TASK=2 tseek -j $SLURM_CPUS_PER_TASK
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] tailseeker.sh