rMAPS consists of two tools. Motif Map performs motif enrichment analysis for RNA-binding proteins. CLIP Map examines CLIP-seq peak data to generate RNA-map of the protein used in the CLIP-seq experiment.
It is a simple step. You can simply select Genome assembly used in the RNA-seq experiment. rMAPS currently supports human (hg38, hg19), mouse (mm10), fly (dm6, dm3), rat (rn6), C. elegans (ce11), zebrafish (danRer10, danRer11), Arabidopsis thaliana (araTha1), frog (xenLae2, xenTro9), and rice (oSa7) are available.
rMAPS supports rMATS outputs, miso outputs, and user-provided coordinates for differential alternative splicing exons and control exons. rMAPS can analyze all 5 major types of alternative splicing events as follows:
Skipped Exon (SE)
Mutually eXclusive Exon (MXE)
Alternative to 5′ Splice Site (A5SS)
Alternative to 3′ Splice Site (A3SS)
Retained Intron (RI)
Exon coordinates are from three exons involved in skipping events.
Exon coordinates are from four exons involved in mutually exclusive events.
Exon coordinates are from three exons involved in alternative to 5′ splicing events.
Exon coordinates are from three exons involved in alternative to 3′ splicing events.
Exon coordinates are from three exons involved in retained intron events.
It typically takes under 4 minutes for all 5 alternative splicing types together.
It typically takes under 1 minute for all 5 alternative splicing types together.