MapSplice

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Description

mapsplice website  

MapSplice MapSplice is an algorithm for mapping RNA-seq data to reference genome for splice junction discovery. Features of MapSplice include:

  1. Alignment of both short reads < 75bp and long reads >= 75bp.
  2. Both CPU and memory efficiency.
  3. Detection of small exons.
  4. Discovery of canonical, semi-canonical and non-canonical junctions.
  5. Splice inference based on the alignment quality and diversity of reads mapped to a junction.
  6. Identification of chimeric events (intra-chromosomes and inter-chromosomes, inter-strands) with long reads.
  7. Identification of chimeric events (intra-chromosomes and inter-chromosomes, inter-strands) with short paired-end reads.
  8. Support paired-end reads and single-end reads

Required Modules

modules documentation

Serial

  • mapsplice

System Variables

  • HPC_MAPSPLICE_DIR - installation directory
  • HPC_MAPSPLICE_BIN - executable directory.




Citation

If you publish research that uses {{{app}}} you have to cite it as follows:

Kai Wang, Darshan Singh, Zheng Zeng, Stephen J. Coleman, Yan Huang, Gleb L. Savich, Xiaping He, Piotr Mieczkowski, Sara A. Grimm, Charles M. Perou, James N. MacLeod, Derek Y. Chiang, Jan F. Prins and Jinze Liu. Nucleic Acids Research 2010; doi: 10.1093/nar/gkq622


Original publication

Validation

  • Validated 4/5/2018