Multivariate Analysis of Transcript Splicing (MATS)
Xing Lab, University of California, Los Angeles
FAQ
Q: What is the difference between MATS and rMATS?
Q: Where is the latest version of MATS or rMATS available?
Q: Can MATS handle replicates?
Q: What if I don't have replicates?
Q: Can rMATS handle strand-specific data?
Q: New version of samtools does not work with rMATS?
Q: Can I run rMATS with TopHat2?
Q: Can I run rMATS with STAR aligner output?
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: Does MATS handle samples with different read lengths?
Q: MATS reported hundreds of significant AS events. Is there any tool to design RT-PCR primers for further validation?
Q: Is there any downstream analysis tool that can directly utilize rMATS output?
Q: Is there a mininum number of replicates required for paired analysis (-analysis P)?
Q: I have further comments/questions. Where can I post them?
Q: What is the difference between MATS and rMATS?
A: MATS compares two samples without replicates while rMATS compares two samples with replicates. MATS is now integrated into the rMATS package. Running rMATS without replicates will automatically invoke MATS algorithm.
Q: Where is the latest version of MATS or rMATS available?
A: http://rnaseq-mats.sourceforge.net/ always has the link to the latest version of MATS or rMATS.
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: Can rMATS handle strand-specific data?
A: Yes! As of version 3.2.0 beta, rMATS can now handle strand-specific data.
A: Yes! As of version 3.2.0 beta, rMATS can now handle strand-specific data.
Q: New version of samtools does not work with rMATS?
A: New version of rMATS (v3.2.0.beta) started supporting samtools v1.2.
A: New version of rMATS (v3.2.0.beta) started supporting samtools v1.2.
Q: Can I run rMATS with TopHat2?
A: The current version of rMATS supports Tophat2 indirectly. Users can map your reads independently (using Tophat2 or any other aligners) then feed rMATS with the resulting bam files. To run rMATS with fastq files, users need to use TopHat 1 and corresponding bowtie indexes. 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: The current version of rMATS supports Tophat2 indirectly. Users can map your reads independently (using Tophat2 or any other aligners) then feed rMATS with the resulting bam files. To run rMATS with fastq files, users need to use TopHat 1 and corresponding bowtie indexes. 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: 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 http://www.mimg.ucla.edu/faculty/xing/public_data/rMATS/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 0.0001 will cause significant events to have larger differences but less events will be significant.
A: Use the -c option. Increasing above the default 0.0001 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 occurred then it will appear in the last few lines of the log file. Also, check samtools to see if it supports -X option.
A: Examine the log file named log.RNASeq-MATS.TimeStamp in the MATS output directory. If an error occurred then it will appear in the last few lines of the log file. Also, check samtools to see if it supports -X option.
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.
Q: Does MATS handle samples with different read length?
A: MATS currently requires all the read lengths to be the same. We are planning to support various read length in the future. Meanwhile, users can use trimFastq.py tool included in the MATS package to trim the reads to the same length.
Q: MATS reported hundreds of significant AS events. Is there any tool to design RT-PCR primers for further validation?
A: Yes, we released a stand-alone primer design tool, PrimerSeq, for designing RT-PCR primers from MATS output. Please check it out.
Q: Is there any downstream analysis tool that can directly utilize rMATS output?
A: Yes, we released a motif enrichment analysis server, rMAPS: RNA Map Analysis and Plotting Server, for the analysis of RNA-binding proteins (RBPs) binding site around the rMATS SE events. Please check it out.
Q: Is there a mininum number of replicates required for paired analysis (-analysis P)?
A: Yes, paired-analysis (-analysis P) option requires at least 3 replicates per sample..
Q: I have further comments/questions. Where can I post them?
A: You can post comments or questions on the rMATS Users Google Group.