MISO on Helix
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.
Programs location
/usr/local/MISO
Important Note
The following environmental variable must be set first:
For bash users:
$ export LD_LIBRARY_PATH=/usr/local/gsl-1.14/lib:$LD_LIBRARY_PATH
$ export PATH=/usr/local/Python/2.7.2/bin:$PATH
For tcsh/csh users:
% setenv LD_LIBRARY_PATH /usr/local/gsl-1.14/lib:$LD_LIBRARY_PATH
% set path=( /usr/local/Python/2.7.2/bin ${path} )
How To Use
Example
$ python sam_to_bam.py --convert my_sample.sam my_sample/ --ref mm9_complete.fa.fai
$ python index_gff.py --index SE.mm9.gff indexed
$ ......
