SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SpliceMap 3.3 Released - Improved long-read sensitivity john_mu Bioinformatics 19 08-08-2011 03:39 PM
How to call "gaps" from spliced read alignment? sulicon Bioinformatics 3 06-09-2011 08:28 AM
Spliced alignment with BWA telos SOLiD 7 10-06-2010 06:32 AM
PubMed: Supersplat -- spliced RNA-seq alignment. Newsbot! Literature Watch 0 05-09-2010 07:00 PM
SpliceMap: New tool for detecting splice junctions from RNA-Seq data jm1234567890 Bioinformatics 10 04-22-2010 07:57 AM

Reply
 
Thread Tools
Old 09-07-2010, 02:34 PM   #1
john_mu
Member
 
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.

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
john_mu is offline   Reply With Quote
Reply

Tags
rna-seq, splice, splice junctions, transcriptomics

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:37 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO