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Old 09-07-2010, 02:34 PM   #1
Location: Stanford, CA

Join Date: May 2010
Posts: 88
Default SpliceMap 3.3.3.x released: Tool for spliced read alignment

Hi Everyone,

SpliceMap 3.3.3.x has been release with many user requested features and stability/reliability enhancements.


The following is a summary of the major changes.
  • High specificity in junction identification
  • Alignments of reads with variable length in both pairs (eg. after trimming)
  • Support for concatenated genome files
  • Bowtie index automatically built if not found
  • Read quality and names copied to SAM file
  • Option to run multiple chromosomes at same time
  • Option to change location of temp and output directories
  • and more... (see website)

A useful feature of SpliceMap I would just like to point out is that each junction is tagged with the number of non-redundant reads so that the reliability of each junction can be judged.

The following is some example output of junctions (not full alignment) from cisGenome browser.

Novel junctions are colored and possibly unreliable ones are colored more lightly.

SpliceMap: De novo detection of splice junctions from RNA-seq
Download SpliceMap Comment here
john_mu is offline   Reply With Quote

rna-seq, splice, splice junctions, transcriptomics

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