Wikiomics:RNA-Seq: Difference between revisions

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===Mapsplice===
===Mapsplice===
http://www.netlab.uky.edu/p/bioinfo/MapSplice/
http://www.netlab.uky.edu/p/bioinfo/MapSplice/
current version: 1.11 2010.5.18
 
current version: 1.13.6  2010.07.29
 
base mapper: bowtie
base mapper: bowtie


==Spliced Mappers (old)==
==Spliced Mappers (old)==

Revision as of 03:24, 29 July 2010

Mappers

Spliced Mappers (tested)

Tophat

http://tophat.cbcb.umd.edu/

current version: 1.0.13 (BETA) from 2/5/2010 base mapper: bowtie

SOAPals

http://soap.genomics.org.cn/soapals.html

current version: 1.1 , 05-05-2010


GEM

http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=The_GEM_library

current version: GEM-binaries-Linux-x86_64-20100419-003425.tbz2 base mapper: GEM split-mapper


SOLiD data only

(untested)

SplitSeek

http://solidsoftwaretools.com/gf/project/splitseek/

current version: 1.3.2

RNA-mate

http://solidsoftwaretools.com/gf/project/rnamate

current version: 1.01

Spliced Mappers (in developement)

Mapsplice

http://www.netlab.uky.edu/p/bioinfo/MapSplice/

current version: 1.13.6 2010.07.29

base mapper: bowtie

Spliced Mappers (old)

ERANGE

http://woldlab.caltech.edu/rnaseq/

current version: 3.1 from 2009/04/17. base mapper: bowtie (see version restriction)

GMORSE

http://www.genoscope.cns.fr/externe/gmorse/ Proper name: G-Mo.R-Se current version: 06-Nov-2009

It was used for Vitis vinifera genome project.

Not spliced

Mapping short reads to draft genome sequence with multiple contigs poses problems for current spliced mappers.

blat

http://genome.ucsc.edu/FAQ/FAQblat.html

last

http://last.cbrc.jp/

Latest: last-128.zip 28-Jun-2010

Installation:

cd src; make