SpliceMap 3.3.3.x released: Tool for spliced read alignment

john_mu

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Join Date: May 2010

Posts: 88
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SpliceMap 3.3.3.x released: Tool for spliced read alignment

09-07-2010, 02:34 PM

Hi Everyone,

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

Website: http://www.stanford.edu/group/wonglab/SpliceMap/

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.

Enjoy!

SpliceMap: De novo detection of splice junctions from RNA-seq
Download SpliceMap Comment here
Tags: rna-seq, splice, splice junctions, transcriptomics

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