Multivariate Analysis of Transcript Splicing (MATS)
Xing Lab, University of California, Los Angeles
FAQ
Q: Where is the latest version of MATS available?
A: http://rnaseq-mats.sourceforge.net/ always has the link to the latest version of MATS.
Q: Can MATS handle replicates?
A: In August, a new version of MATS will be released to handle replicates.
Q: I have problem downloading Bowtie indexes for human and mouse.
A: Some browsers have a limit on downloadable file size. Use a different browser or download indexes directly from Linux command line.
wget ftp://mats:@intron.healthcare.uiowa.edu/bowtieIndexes.tgz
Q: Does MATS work with MacOS?
A: Unfortunately, MacOS is not supported yet.
Q: How do I run MATS for poorly annotated species? No GTF file is available for the species.
A: Use cufflinks GTF files as input for MATS
Q: How can I change the the user-defined difference in isoform ratios?
A: Use the -c option. Increasing above the default 0.05 will cause significant events to have larger differences but less events will be significant.