Multivariate Analysis of Transcript Splicing (MATS)
Xing Lab, University of California, Los Angeles
FAQ
Q: Where is the latest version of MATS available?
Q: Can MATS handle replicates?
Q: What if I don't have replicates?
Q: I have problem downloading Bowtie indexes for human and mouse.
Q: Does MATS work with MacOS?
Q: How do I run MATS for poorly annotated species? No GTF file is available for the species.
Q: How do I get the insert size mean and standard deviation for paired-end data?
Q: How can I change the the user-defined difference in isoform ratios?
Q: I did not get correct output, what should I do?
Q: There is no MATS output and the log file did not record any errors, what should I do?
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: Yes! As of version 3.0.0 beta, MATS can now handle replicates.
A: Yes! As of version 3.0.0 beta, MATS can now handle replicates.
Q: What if I don't have replicates?
A: MATS 3.X.X can handle both non-replicates and replicates.
A: MATS 3.X.X can handle both non-replicates and 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.
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: Yes! MATS 3.X.X works with both Linux and MacOS.
A: Yes! MATS 3.X.X works with both Linux and MacOS.
Q: How do I run MATS for poorly annotated species?
A: Use cufflinks GTF files as input for MATS
A: Use cufflinks GTF files as input for MATS
Q: How do I get the insert size mean and standard deviation for paired-end data?
A: We recommend use of other software such as Picard to get the insert size mean and standard deviation rather than relying on the default value of MATS. The -r1 and -r2 options specify the mean insert size and the -sd1 and -sd2 options specify the insert size standard deviation (see user guide for more detail).
A: We recommend use of other software such as Picard to get the insert size mean and standard deviation rather than relying on the default value of MATS. The -r1 and -r2 options specify the mean insert size and the -sd1 and -sd2 options specify the insert size standard deviation (see user guide for more detail).
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.
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.
Q: If I did not get correct output, what should I do?
A: Examine the log file named log.RNASeq-MATS.TimeStamp in the MATS output directory. If an error occured then it will appear in the last few lines of the log file.
A: Examine the log file named log.RNASeq-MATS.TimeStamp in the MATS output directory. If an error occured then it will appear in the last few lines of the log file.
Q: There is no MATS output and the log file did not record any errors, what should I do?
A: A common cause is non-consistent chromosome names in the GTF file and the bowtie index. See here for details.