PARpipe is a complete analysis pipeline for PAR-CLIP data providing the following features:
- Pre-processing and alignment of reads
- Definition of interaction sites using PARalyzer v1.5 (download)
- Additional site-level metrics
- Annotation of reads, groups, and cluster
- Meta-analysis of binding sites relative to important transcript features
Example files are under /usr/local/apps/parpipe/current/test directory.
To test with the example files:
$ cp -r /usr/local/apps/parpipe/current/test /data/$USER $ cd /data/$USER/test $ sinteractive --mem=5g $ module load parpipe $ bpipe run -r /usr/local/apps/parpipe/current/parclip_pipe.sh ./test.fastq
Sample session:
[helix ~]$ module load parpipe [helix ~]$ bpipe run -r /usr/local/apps/parpipe/current/parclip_pipe.sh ./test.fastq
Create a batch input file (e.g. script.sh). For example:
#!/bin/bash module load parpipe cd /data/$USER/dir parpipe command 1 parpipe command 2 ......
Then submit the file on biowulf
biowulf> $ sbatch script.sh
For more information regarding sbatch command : https://hpc.nih.gov/docs/userguide.html#submit
Create a swarmfile (e.g. script.swarm). For example:
# this file is called script.swarm cd dir1;parpipe command 1; parpipe command 2 cd dir2;parpipe command 1; parpipe command 2 cd dir3;parpipe command 1; parpipe command 2 [...]
Submit this job using the swarm command.
swarm -f script.swarm --module parpipe
For more information regarding swarm: https://hpc.nih.gov/apps/swarm.html#usage
Allocate an interactive session. Sample session:
[biowulf ~]$ sinteractive --mem=5g salloc.exe: Pending job allocation 15194042 salloc.exe: job 15194042 queued and waiting for resources salloc.exe: job 15194042 has been allocated resources salloc.exe: Granted job allocation 15194042 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn1719 are ready for job [cn1719 ~]$ module load parpipe [cn1719 ~]$ parpipe command
