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 on in-house data.
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
The SOAPals website provides exact informations how to install and run it.
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)
PALMapper (fusion of GenomeMapper & QPALMA)
http://www.fml.tuebingen.mpg.de/raetsch/suppl/palmapper current version: palmapper-0.4-rc3.tar.gz 05/09/10
Simple installation (run "make" in installation directory). To check the install go to "testcase" and run "make" again. This requires fast Internet connection as it downloads genome files. Output files in a tabulated, but no gff format.
Creating index:
pmindex -i genome_file.fa -v
Command used to map testcase:
palmapper -i data/c_elegans.WS209.dna.fa -q data/split_1m.000 -acc data/C_elegans_SpliceSitePred_WS209/acc_pred.bspf/contig_%i%c -don data/C_elegans_SpliceSitePred_WS209/don_pred.bspf/contig_%i%c -o data/split_1m.000.mapped -u data/split_1m.000.unmapped -H data/split_1m.000.spliced -filter-max-mismatches 3 -filter-max-gaps 0 -filter-splice-min-edit 2 -filter-splice-region 5 -f bedx -qpalma data/parameters.qpalma -qpalma-use-map-max-len 2000 -report-map-read -report-spliced-read -report-map-region -report-splice-sites 0.9 -M 6 -G 2 -E 6 -l 18 -L 35 -K 12 -C 55 -I 25000 -NI 2 -SA 5 -CT 10 -z 10 -S -seed-hit-cancel-threshold 10000"
CAVEAT: It requires QPALMA parameter files. These seem to be both species and tissue specific, plus there is a distinction between paired vs unpaired parameter files i.e. human_HepG2_left_l75.qpalma. For creating these one needs to install QPALMA itself (unsuccessful install in the past, not tested recently).
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
requirements: min 2GB RAM/mammalian genome, 16-20GB recommended for optimal performance
Installation:
cd src; make
Creating genomic database and short reads mapping:
#db creation lastdb -m1111110 -s20G -v my_genome_db my_genome.fasta #mapping lastal -Q1 -o reads_vs_my_genome_db.out -f 0 -v my_genome_db reads.fastq
where: -Q1: fastq format -f 0: output in tabulated format -v: verbose (prints what it is doing)
last can map reads with indels and truncate large parts of the reads (highly sensitive but with lower specificity). Output needs to be filtered from spurious matches.
