Wikiomics:RNA-Seq
Mappers
Spliced Mappers (tested)
Tophat
current version: 1.1.4 release 2010.11.16
base mapper: bowtie input: fastq output: BAM
Currently the most widely used program for RNA-Seq mapping. Output often processed with Cufflinks.
HMMSplicer
http://derisilab.ucsf.edu/index.php?software=105
current version: 0.9.5 2010.11.25 base mapper: bowtie input: fastq (converts quality values to phred scale) output: bed file of junctions
Developed in Python. Requirements:
- OS: tested on MacOS X (authors), Linux Fedora 8,
- Python 2.6 (tested with 2.6.4)
- numpy (tested by authors with version 1.3.0)
- bowtie (works with 0.12.7)
Also completes running example with Python 2.7.1rc1, numpy-1.5.1 and bowtie 0.12.7.
Basic command:
python runHMM.py -o output_dir -i input_RNA-seq_data.qseq -q quality_type -g genome4mapping -j min_intron_size -k max_intron_size -p number_of_procesors_to_use
type: python runHMM.py --help for more explanation
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
Developed in Erlang and Python. Two step mapping (unspliced mode first, then unmapped reads are mapped with splicing).
GMAP/GSNAP
http://research-pub.gene.com/gmap/
current version: 2010-07-27
FastA and FASTQ input, support for paired ends.
ERANGE
http://woldlab.caltech.edu/rnaseq/
current version: 3.2.1 from 2010.08.10
base mapper: bowtie or blat
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)
QPALMA
http://www.fml.tuebingen.mpg.de/raetsch/suppl/qpalma
current version: 0.9.2 (release candidate 1) 2010.05.08
Number of requirements, installation unsuccessful.
Mapsplice
http://www.netlab.uky.edu/p/bioinfo/MapSplice/
current version: MapSplice 1.14.1 2010.09.30
base mapper: bowtie
SpliceMap
http://www.stanford.edu/group/wonglab/SpliceMap/
current version: 3.3.5.2 2010.10.23
base mapper (preferred): bowtie (others possible) "Currently, only the cannoical GT-AG splice sites are identified."
TAU
http://mocklerlab-tools.cgrb.oregonstate.edu/TAU.html
current version: 1.4 2010.09.06
SAW (method no software yet)
Ning K, Fermin D (2010) SAW: A Method to Identify Splicing Events from RNA-Seq Data Based on Splicing Fingerprints. PLoS ONE 5(8): e12047. doi:10.1371/journal.pone.0012047
Spliced Mappers (old)
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
Latest: last-146.zip 18-Nov-2010
Installation:
cd src; make
