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Spats on Biowulf and Helix

Spats processes reads and calculates SHAPE reactivities for SHAPE-Seq experiments on multiple RNAs. It accepts raw paired-end sequencing reads in fastq format, and a target sequence file containing the sequences of RNAs present in the experimental pool. Spats then performs read alignment to calculate distributions of read ends in the SHAPE (+) and (-) channel for each nucleotide in each RNA. Spats then estimates nucleotide resolution SHAPE reactivities for each RNA, using a model-driven maximum likelihood procedure based on a model of the reverse transcriptase process used in the SHAPE-Seq experiment. Spats is a collaborative effort between the Aviran Lab at UC Davis, the Pachter Lab at UC Berkeley, the Trapnell Lab at the University of Washington, and the Lucks Lab at Cornell University. 




Running on Helix

Sample session:

helix$ module load spats
helix$ spats
 Spats builds reactivity profiles from SHAPE-Seq experiments.

     spats [options] rna.fasta treated_handle untreated_handle reads1[,reads2,...,readsN] reads1[,reads2,...,readsN]

     -o/--output-dir                (string)    [ default: ./spats_out ]
     --adapter-t                 (string)    [ default: None ]
     --adapter-b                (string)    [ default: None ]
     --trim-match               (int)       [default: 9]
     --num-mismatches               (int)       [ default: 0    ]

SAM Header Options (for embedding sequencing run metadata in output):
    --rg-id                        (string)    (read group ID)
    --rg-sample                    (string)    (sample ID)
    --rg-library                   (string)    (library ID)
    --rg-description               (string)    (descriptive string, no tabs allowed)
    --rg-platform-unit             (string)    (e.g Illumina lane ID)
    --rg-center                    (string)    (sequencing center name)
    --rg-date                      (string)    (ISO 8601 date of the sequencing run)
    --rg-platform                  (string)    (Sequencing platform descriptor)

    for detailed help see http://spats.sourceforge.net/

Submitting a single batch job

1. Create a script file. The file will contain the lines similar to the lines below. Modify the path of program location before running.


module load spats
cd /data/$USER/somewhere
spats [options] rna.fasta treated_handle untreated_handle reads1[,reads2,...,readsN] reads1[,reads2,...,readsN]

2. Submit the script on Biowulf.

$ sbatch myscript

Submitting a swarm of jobs

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile). Here is a sample file:

cd /data/user/run1/; spats command
cd /data/user/run2/; spats command
cd /data/user/run10/; spats command

The -f flag is required to specify swarm file name.

Submit the swarm job:

$ swarm -f swarmfile --module spats

For more memory requirement (default 1.5gb per line in swarmfile), use -g flag

$ swarm -g 4 -f swarmfile --module spats

For more information regarding running swarm, see swarm.html


Running an interactive job

User may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

[user@biowulf]$ sinteractive 

[user@pXXXX]$ cd /data/$USER/myruns

[user@pXXXX]$ module load spats

[user@pXXXX]$ cd /data/user/run1/; spats command

[user@pXXXX] exit
slurm stepepilog here!