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Vasttools on NIH HPC Systems

A toolset for profiling alternative splicing events in RNA-Seq data.

Contributions

  • Manuel Irimia
  • Nuno Barbosa-Morais
  • Ulrich Braunschweig
  • Sandy Pan
  • Kevin Ha
  • Tim Sterne-Weiler

Citation

  • VAST-TOOLS:
    Irimia, M., Weatheritt, R.J., Ellis, J., Parikshak, N.N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallières, M., Tapial, J., Raj, B., O’Hanlon, D., Barrios-Rodiles, M., Sternberg, M.J.E., Cordes, S.P., Roth, F.P., Wrana, J.L., Geschwind, D.H., Blencowe, B.B. (2014). A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell, 59:1511-23.
  • Intron retention analysis:
    Braunschweig, U., Barbosa-Morais, N.L., Pan, Q., Nachman, E., Alipahani, B., Gonatopoulos-Pournatzis, T., Frey, B., Irimia, M., Blencowe, B.J. (2014). Widespread intron retention in mammals functionally tunes transcriptomes. Genome Research, 24:1774-86
  • Chicken database:
    Gueroussov, S., Gonatopoulos-Pournatzis, T., Irimia, M., Raj, B., Lin, Z.Y., Gingras, A.C., Blencowe, B.J. (2015). An alternative splicing event amplifies evolutionary differences between vertebrates. Science, 349:868-73

Batch job on Biowulf

Create a batch input file (e.g. script.sh). For example:

#!/bin/bash
module load vasttools

cd /data/$USER/dir
vast-tools align tissueA_rep1.fq.gz
vast-tools align tissueA_rep2.fq.gz
vast-tools align tissueB_rep1.fq.gz
vast-tools align tissueB_rep2.fq.gz
......

Then submit the file on biowulf

biowulf> $ sbatch script.sh

For more information regarding sbatch command : https://hpc.nih.gov/docs/userguide.html#submit

Swarm of Jobs on Biowulf

Create a swarmfile (e.g. script.swarm). For example:

# this file is called script.swarm
cd dir1;vast-tools command 1;vast-tools command 2
cd dir2;vast-tools command 1;vast-tools command 2
cd dir3;vast-tools command 1;vast-tools command 2
[...]

Submit this job using the swarm command.

swarm -f script.swarm --module vasttools

For more information regarding swarm: https://hpc.nih.gov/apps/swarm.html#usage

Interactive job on Biowulf

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 vasttools

[cn1719 ~]$ vasttools command

Documentation

https://github.com/vastgroup/vast-tools