rMATS pipeline

rMATS specifications

Information


Unique identifier OMICS_01336
Name rMATS
Alternative names replicate Multivariate Analysis of Transcript Splicing, MATS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format (FASTQ, BAM) + GTF
Output data Alternative Splicing events sorted by P-values in ascending order
Output format TXT
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 3.2.5
Stability Stable
Requirements STAR, Samtools, Numpy, Scipy, Pysam
Maintained Yes

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Documentation


Publications for replicate Multivariate Analysis of Transcript Splicing

rMATS IN pipelines

 (11)
2018
PMCID: 5955895
PMID: 29769602
DOI: 10.1038/s41598-018-26035-x

[…] small numbers of replicates at each time point., raw sequencing reads were first mapped to the rat genome using star30 2.5.2a with the 2-pass option. the resulting 2-pass bam files were processed by rmats19 for exon inclusion level differences between lean and obese groups at each time point. both exon–exon junction reads and the reads that mapped to the exons were used in the analyses. […]

2017
PMCID: 5501815
PMID: 28687784
DOI: 10.1038/s41598-017-05377-y

[…] we calculated transcript length, exon number and gc content using in-house perl scripts. to identify as events in our transcriptomes, we used the bam files from the star as the input files for the rmats (v3.0.9)58. all parameters of rmats were set as default values., we used rsem (v1.2.17) to calculate read counts from the output of bam files46. expression estimates in units of fpkm […]

2017
PMCID: 5501815
PMID: 28687784
DOI: 10.1038/s41598-017-05377-y

[…] number and gc content using in-house perl scripts. to identify as events in our transcriptomes, we used the bam files from the star as the input files for the rmats (v3.0.9)58. all parameters of rmats were set as default values., we used rsem (v1.2.17) to calculate read counts from the output of bam files46. expression estimates in units of fpkm were obtained after normalizing the count […]

2017
PMCID: 5529932
PMID: 28789374
DOI: 10.3892/ol.2017.6300

[…] (hg19), based on tophat, and were assembled into transcripts via cufflink. the differential expression (de) and differential alternative splicing (das) genes were screened out through cuffdiff and rmats, respectively. the significantly enriched gene ontology (go) terms and kyoto encyclopedia of genes and genomes pathways were obtained through the database of annotation, visualization […]

2017
PMCID: 5702118
PMID: 29178824
DOI: 10.1186/s12864-017-4310-5

[…] method was used to construct and identify both known and novel transcripts from tophat alignment results [40]. alternative splicing (as) events were classified to five major types by the software rmats (multivariate analysis of transcript splicing) v3.2.5 [41]. the number of as events in each sample was estimated separately. because the chicken genome has been recently updated [42], […]

rMATS institution(s)
Departments of Microbiology, Immunology, and Molecular Genetics and Departments of Molecular Physiology and Biophysics and Pathology, University of Iowa, Iowa City, IA, USA; Statistics, University of California, Los Angeles, CA, USA; Departments of Microbiology, Immunology, & Molecular Genetics, USA

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