Sicer is a clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Sicer2 is redesigned and improved ChIP-seq broad peak calling tool from SICER.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive 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 sicer [user@cn3144 ~]$ cd /data/$USER/sicer [user@cn3144 ~]$ cp -r /usr/local/apps/sicer/2-1.0.3/SICER2/test . [user@cn3144 ~]$ sicer_df -t treatment_1.bed treatment_2.bed \ -c control_1.bed control_2.bed \ -s hg38 --significant_reads [user@cn3144 ~]$ recognicer_df -t treatment_1.bed treatment_2.bed \ -c control_1.bed control_2.bed \ -s hg38 --significant_reads [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. batch.sh). For example:
#!/bin/bash set -e module load sicer sicer_df -t treatment_1.bed treatment_2.bed \ -c control_1.bed control_2.bed \ -s hg38 --significant_reads
Submit this job using the Slurm sbatch command.
sbatch [--mem=#] batch.sh
Create a swarmfile (e.g. job.swarm). For example:
cd dir1; sicer_df... cd dir2; sicer_df... cd dir3; sicer_df...
Submit this job using the swarm command.
swarm -f job.swarm [-g #] --module sicerwhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| --module | Loads the module for each subjob in the swarm |