NGS RNA-Seq

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This page summarizes RNA-seq related activities carried out by the NGS taskforce member groups.

Experts

Need a local expert on RNA-Seq? Maybe one of the following names can help you.

  • Peter-Bram ‘t Hoen (LUMC)
  • Marieke Simonis (Hubrecht/UMCU)
  • Yanju Zhang (LUMC)

NBIC tools

  • PASSion: a pattern growth based algorithm for splice site detection from paired-end RNA-Seq reads.

NBIC courses

Evaluation of RNA tools

Work performed by Irina Pulyakhina (LUMC)

Tool Which algorithm/tool is used for mapping Does the tool detect canonical/non-canonical splice sites Speed (reads mapped per hour on a single thread) Sensitivity Specificity Does the tool use paired-end information The most appropriate for the tool application The weak parts of the tool Last update of the source code Is the tool able to detect multiple splice events per single read Does the tool search fpr novel splicing sites Is the tool multi-thread Link to the paper
GSNAP indexing the reference and the reads; looking for overlaps in two index tables canonical and non-canonical splice junctions 500000 yes pre-mRNA prioritize intron alignments to exon alignments 23-03-2012 yes yes yes article
HMMSplicer bowtie (alignment) + hidden Markov model (detection of a splice junction) canonical and non-canonical splice junctions 2.2 mln yes low-abundance transcripts, low sequence quality 25-11-2010 no yes no info article
MapSplice first segment exonic alignment, then segment spliced alignment, then segment assembly canonical and non-canonical splice junctions 100 mln yes aligning splice junctions de novo 12/04/12 yes yes yes article
PASSion pattern-growth algorithm canonical and non-canonical splice junctions no info yes splicings mediating across chromosome gene fusion 12/01/11 yes yes yes article
SpliceMap half-read mapping, finding exonic hits, searching for junctions canonical splice junctions 30 mln yes 10/01/10 no yes no info article
SplitSeek mapping pieces of fragments of reads (anchors) and extending anchor alignments canonical splice junction no info yes Abi Solid reads only Abi Solid reads 19-11-2010 no yes no article
TopHat bowtie + partitioning unmapped reads canonical and non-canonical splice junctions 2.2 mln yes 02/02/12 no yes yes article