Multivariate Analysis of Transcript Splicing (MATS)
Xing Lab, Children's Hospital of Philadelphia
FAQ
Q: What are the differences between rMATS v4.*.* (turbo) and earlier versions?
Q: Can rMATS handle replicates?
Q: What if I don't have replicates?
Q: Can rMATS handle strand-specific data?
Q: Can I run rMATS with TopHat2?
Q: Can I run rMATS with STAR aligner output?
Q: Does rMATS work with MacOS?
Q: How do I run rMATS for poorly annotated species?
Q: How can I change the user-defined difference in isoform ratios?
Q: How to install rMATS and dependencies for it?
Q: Can I turn off the statistical model? I just want to get the read count and Alternative Splicing Event.
Q: Can rMATS handle replicates?
Q: What if I don't have replicates?
Q: Can rMATS handle strand-specific data?
Q: Can I run rMATS with TopHat2?
Q: Can I run rMATS with STAR aligner output?
Q: Does rMATS work with MacOS?
Q: How do I run rMATS for poorly annotated species?
Q: How can I change the user-defined difference in isoform ratios?
Q: How to install rMATS and dependencies for it?
Q: Can I turn off the statistical model? I just want to get the read count and Alternative Splicing Event.
Q: What are the differences between rMATS v4.*.* (turbo) and earlier versions?
A: rMATS turbo is the C/Cython version of rMATS. The major difference between rMATS turbo and rMATS is speed and space usage. rMATS turbo is 100 times faster and the output file is 1000 times smaller than rMATS. These advantages make analysis and storage of a large scale dataset easy and convenient. For more details about changes between versions see the Updates section.
A: rMATS turbo is the C/Cython version of rMATS. The major difference between rMATS turbo and rMATS is speed and space usage. rMATS turbo is 100 times faster and the output file is 1000 times smaller than rMATS. These advantages make analysis and storage of a large scale dataset easy and convenient. For more details about changes between versions see the Updates section.
Q: Can rMATS handle replicates?
A: Yes, replicates are specified in files used for the --b1 and --b2 (or --s1 and --s2) command line arguments.
A: Yes, replicates are specified in files used for the --b1 and --b2 (or --s1 and --s2) command line arguments.
Q: What if I don't have replicates?
A: Just specify whatever read files you want to compare using the --b1 and --b2 (or --s1 and --s2) command line arguments. Even if you only have a single read file you can still get the alternative splicing event counts by using --statoff and only specifying --b1 (or --s1).
A: Just specify whatever read files you want to compare using the --b1 and --b2 (or --s1 and --s2) command line arguments. Even if you only have a single read file you can still get the alternative splicing event counts by using --statoff and only specifying --b1 (or --s1).
Q: Can rMATS handle strand-specific data?
A: Yes, use the --libType command line argument.
A: Yes, use the --libType command line argument.
Q: Can I run rMATS with TopHat2?
A: rMATS supports Tophat2 indirectly. Users can map their reads independently (using Tophat2 or any other aligners) then feed rMATS with the resulting BAM files. We strongly recommend that users map reads independently using their choice of aligner (including Tophat2) to reduce the rMATS running time and to preserve their own mapping procedures.
A: rMATS supports Tophat2 indirectly. Users can map their reads independently (using Tophat2 or any other aligners) then feed rMATS with the resulting BAM files. We strongly recommend that users map reads independently using their choice of aligner (including Tophat2) to reduce the rMATS running time and to preserve their own mapping procedures.
Q: Can I run rMATS with STAR aligner output?
A: STAR aligner performs soft clipping by default which will generate variable read lengths. You can run STAR with "--alignEndsType EndToEnd" option to suppress soft clipping.
A: STAR aligner performs soft clipping by default which will generate variable read lengths. You can run STAR with "--alignEndsType EndToEnd" option to suppress soft clipping.
Q: Does rMATS work with MacOS?
A: rMATS is tested only with Linux. You may try building from the source code, but some modifications may be needed.
A: rMATS is tested only with Linux. You may try building from the source code, but some modifications may be needed.
Q: How do I run rMATS for poorly annotated species?
A: Use cufflinks GTF files as input for rMATS.
A: Use cufflinks GTF files as input for rMATS.
Q: How can I change the user-defined difference in isoform ratios?
A: Use the --cstat command line argument. Increasing above the default 0.0001 will cause significant events to have larger differences, but fewer events will be significant.
A: Use the --cstat command line argument. Increasing above the default 0.0001 will cause significant events to have larger differences, but fewer events will be significant.
Q: How to install rMATS and dependencies for it?
A: See the README in the source code repo.
A: See the README in the source code repo.
Q: Can I turn off the statistical model? I just want to get the read count and Alternative Splicing Event.
A: Yes, you can use the --statoff command line argument to skip the statistical model. This also allows you to run with a single sample (--b1 without --b2, or --s1 without --s2).
A: Yes, you can use the --statoff command line argument to skip the statistical model. This also allows you to run with a single sample (--b1 without --b2, or --s1 without --s2).