MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.

References:

• The MISO framework is described in Katz et. al., Analysis and design of RNA sequencing experiments for identifying isoform regulation.  Nature Methods (2010).

• http://miso.readthedocs.org/en/fastmiso/

• Module Name: misopy (see the modules page for more information)
• Multithreaded/parallel
• miso_setting.txt
  
  The default miso setting files can be copied from /usr/local/apps/misopy/miso_settings.txt and modified. It looks like this:

  [data]
  filter_results = True
  min_event_reads = 20
  
  [cluster]
  cluster_command = sbatch --mem=20g --cpus-per-task=8 --time=99:00:00
  
  [sampler]
  burn_in = 500
  lag = 10
  num_iters = 5000
  num_chains = 6
  num_processors = 8
  

  Miso can be run in two modes: multi-threaded mode and parallel mode. Each mode use/ignore different directives in the miso setting file.

  Multi-threaded mode will be used when running miso without '--use-cluster' flag.
  The line 'num_processors' will be used and 'cluster_command" will be ignored. The default threads are 8.

  Parallel mode will be used when running miso with both '--use-cluster' and '--chunk-jobs' flags on biowulf. In this mode, depending on the number assigned to '--chunk-jobs=#', many jobs will be submitted to the cluster and each job will use one thread no matter what is assigned to 'num_processors' line since this line will be ignored. Events will beatch and each batch will be submitted to a job. The smaller the # is, the more number of jobs will be created. The default memory is 20gb and 99 hours of walltime for each job. If more memory or walltime is needed, copy/modify the setting file, include '--settings-filename=The_Full_Path_to_Settingfile' flag in miso command, then submit miso job using sbatch.

  If '--settings-filename=.....' flag is not specified in miso command, the default miso setting file will be used.

[user@biowulf]$ sinteractive  --mem=20g --cpus-per-task=8
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 misopy
[user@cn3144 ~]$ miso --run ./indexed ./accepted_hits.bam --output-dir miso_out --read-len 76
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

#!/bin/bash
set -e
module load misopy
cd dir
miso --run ./indexed ./accepted_hits.bam --output-dir miso_out --read-len 76

sbatch --cpus-per-task=8 --mem=20g batch.sh

cd dir1; miso --run ./indexed ./accepted_hits.bam --output-dir miso_out --read-len 76
cd dir2; miso --run ./indexed ./accepted_hits.bam --output-dir miso_out --read-len 76
cd dir3; miso --run ./indexed ./accepted_hits.bam --output-dir miso_out --read-len 76

swarm -f job.swarm -g 20 -t 8 --module misopy

#!/bin/bash
module load misopy
cd /data/$USER/dir
miso --run \
./indexed \
./accepted_hits.bam \
--output-dir miso_out_cluster \
--read-len 76 \
--use-cluster \
--chunk-jobs=1000

$ sbatch jobscript