RNA-Seq data and analysis

RNA Seq datasets

RNA-seq Mapping

Programs for mapping short-reads to a reference genome are available in the "Resequencing" section. Programs that do "spliced-alignment" (allowing for intron-exon junction identification) are classified here.

  • QPALMA: a Vmatch based mapping program using also SVM-based splice site prediction (training needed).

  • TopHat: a BowTie based pipeline for mapping RNASeq to genome with splice site detection.

Transcriptome assembly with RNA-seq

Transcriptome assembly has been tackled using existing 'de novo' assemblers. The main difference lies in the strong variability of sequencing depth (related to expression levels) that makes the assembly more tricky.

RNA Seq expression profiling tools

  • Cufflinks:transcriptime assembly and expression estimation. Still in beta.

RNA Seq/EST CDS prediction

  • ESTScan Predicts ORFs in draft mRNA-seq.

  • FrameDP Orf prediction pipeline for draft mRNA-seq.

Small RNA analysis in RNASeq