MapSplice 1.x





 MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
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; Jinze Liu
Nucleic Acids Research 2010; doi: 10.1093/nar/gkq622


Recent News

2011.9.15  MapSplice is reviewed in Gregory Grant, et. al "Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM)".  It scores highest among RNA-seq aligners not depending on annotations.

2011.5.25 MapSplice 1.15.2 macos

Mac OSX version of MapSplice

2011.4.12 MapSplice 1.15.2

Bugs fix:

(1) fix wrong --, -+ original fusion alignment, and original fusion junction in fusion.junction

(2) In a rare case, few normal junctions are generated

2011.3.26 MapSplice 1.15.1

Fix possbile failure of single anchored fusion mapping step when --cluster, --fusion, --paired are specified at same time, and --non-canonical or --semi-canonical are not specified (output only canonical normal junction) 

2011.3.11 MapSplice 1.15 

1. Find fusion alignments with a single anchored method ( Option --cluster | do_cluster)
2. Add two new kinds of fusion alignments
    (1) Read alignment contain both fusion splice and normal splice
    (2) Fusion alignment across same chromosome, same strand, with short intron length. It is similar to normal splice alignment but the order of aligned segment is reversed. An example is given below.

3. Add fusion remap step
4. Filter fusion junction if doner sequence and acceptor sequence appear repeatedly in the genome. (Option --filter-fusion-by-repeat | filter_fusion_by_repeat)
5. Annotate fusion junction and normal junction to provided transcript file (Option --annotgene | do_annot_gene)
6. Add an option to output fusion non-canonical and semi-canonical junction
7. Support variable read length, read length option (-w | read_length) is no longer needed
8. Support bowtie 0.12.7, use -best option and remove -m option to report best segment alignments if there are repeated segment alignments (more than the threshold set by -max-hits)
9. Output XS:A tag in sam file.  Splice with flank string GTAG, ATAC, GCAG are XS:A:+ , and  CTAC, GTAT, CTGC are XS:A:-. Non-canonical splice is XS:A:+
10.  Support input reads file from bam file and sam file (-M and -bam | sam_file and BAM)
11. Add read format checking
    (1) two ends of a paired end read have same base read name
    (2) pair end read's name end with /1 or /2
    (3) quality string and read sequence length matches
(4) read name don't contain blank string
12. Bug fixes:
    (1) Quality string not correct in unmapped read in alignment.sam
    (2) Temp directory not created when the input data is large 

2010.9.30 MapSplice 1.14.1

MapPER supports all bits of flag tag in input sam files

2010.9.20 MapSplice 1.14

1. Add the alignment with small indels
2. Integrate MapPER v0.12
3. Standardize SAM file format. The alignments are in sorted order, forward alignments come before reverse alignments. Unaligned reads are included as part of the SAM file. IH/HI tags are used to indicate when a read is aligned to multiple places.  Use all bits in flag tag for paired-end reads
4. More filtering added for paired multiple aligned reads.
5. Add chromosome file format checking
6. Fix a few minor bugs

2010.8.18: MapSplice Minor bug fix: filter multiple unspliced alignments when map_segment_directly = no for single end reads. MapPER fix wrong boundaries of some alignments in output sam file.

2010.7.19: MapSplice 1.13.5  Support running mapsplice with a configuration file 

2010.7.14: MapSplice 1.13.4  Fix bug for fasta reads. Add -t/--avoid-regions and -T/--interested-regions to avoid and search in specified regions

2010.7.8:  Source code of  MapSplice 1.13.3 is released.

2010.4.25: This website is under active construction to improve its usability.





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