Performs Transcript Expression Gene
Tool split-read reconstruction Analysis expression
alignment (assembly) (any) analysis
Alexa-Seq N N Y Y
Cufflinks N Y Y Y
Scripture N Y Y N
SpliceMap N N Y Y
TopHat Y N N N
MMES Y N N N
G-Mo.R-Se Y Y N N
SplitSeek Y N N N
GSNAP Y Y N N
* Transcript expression values are non-parsimonious
** Not supported (current version not stable)
Performs Transcript Expression Gene
Tool split-read reconstruction Analysis expression
alignment (assembly) (any) analysis
Alexa-seq N N Y Y
Cufflinks N Y Y Y
Scripture N Y Y N
SpliceMap N N Y Y
TopHat Y N N N
MMES Y N N N
G-Mo.R-Se Y Y N N
SplitSeek Y N N N
GSNAP Y Y N N
* Transcript expression values are non-parsimonious
** Not supported (current version not stable)
Quantitative
Transcript specific Exon junction Expression level
alternative expression
expression analysis expression sensitivity
analysis
Y Y Y Junction
Y N Y Transcript
N* N N Transcript*
N Y N Junction
N Y N Junction
N Y N Junction
N N N Transcript*
N Y N Junction
N N N N/A
Quantitative
Transcript specific Exon or Junction Expression level
alternative expression
expression analysis expression sensitivity
analysis
Y Y Y Junction
Y N Y Transcript
N* N N Transcript*
N Y N Junction
N Y N Junction
N Y N Junction
N N N Transcript*
N Y N Junction
N N N N/A
Minimum read length
Output required or
recommended
Expression and structure information for junctions and
No minimum (tested on
genes; UCSC track info, extensive alternative expression
36bp-100bp reads)
visualization / statistics / graphs
Transcript information and expression statistics, BED, GTF 75bp
Transcript structure information and non-parsimonious
75bp
expression statistics, BED
Alignments. SAM, BED, Wig 50bp
Alignments. SAM, BED, Wig 75bp
Identified splice junctions and p-values 25bp
Transcript structure information. GFF 25bp
Alignments. BED 50bp
Minimum 14bp (tested on
Alignments. SAM and FASTA
36bp reads)
Minimum read length
Output required or
recommended
Expression and structure information for junctions and
No minimum (tested on
genes; UCSC track info, extensive alternative expression
36bp-100bp reads)
visualization / statistics / graphs
Transcript information and expression statistics, BED, GTF 75bp
Transcript structure information and non-parsimonious
75bp
expression statistics, BED
Alignments. SAM, BED, Wig 50bp
Alignments. SAM, BED, Wig 75bp
Identified splice junctions and p-values 25bp
Transcript structure information. GFF 25bp
Alignments. BED 50bp
Minimum 14bp (tested on
Alignments. SAM and FASTA
36bp reads)
Performs comparisons Relevant
Visualization tool between conditions (ex. comparison to
tumor vs normal) Alexa-seq
Extensive, includes
custom graphs and links Y -
to UCSC browser
UCSC browser Y Y
UCSC browser N N
UCSC browser N N
N N N
N N N
Grape Genome Browser N N
UCSC browser N N
UCSC browser N N
Ability to identify
rearrangements / Junction Identification Implementation
indels
N Database Perl/R/Unix
N Predicted from data C++
N Predicted from data Java
N Predicted from data Python
N Predicted from data C++/Python
Published algorithm
N Predicted from data
only
N Predicted from data Perl
Y Predicted from data Perl
Source code in C,
Database or predicted form
Y utility programs in
data
Perl
Data type
Citation
supported
Illumina In preparation
Trapnell et al., 2010,
Paired-end
Nat. Biotech., 28:511-
Illumina reads
515
Guttman et al., 2010,
Illumina Nature Biotech, 28:503-
510 |
http://www.nature.com/
Au et al., 2010, NAR,
Illumina DOI
10.1093/nar/gkq211 |
http://www.stanford.ed
Trapnell C, Pachter L,
Illumina Salzberg SL. 2009,
Bioinformatics,
Wang et al., Plos |
25(9):1105-1111One,
Illumina 2010, Vol 5, Iss 1,
e8529
Denoeud et al., 2008,
Illumina Genome Biol,
9(12):R175 |
http://genomebiology.co
Ameur et al.2010,
SOLiD only Genome Biol.,
11(3):R34. |
Illumina | sodium http://genomebiology.co
Wu and Nacu, 2010,
bisulfite-treated Bioinformatics,
DNA sequencing 26(7):873-881 |
(for analysis of http://bioinformatics.oxf
Validated
Public tool Open Source
events
88% of 192
Y Y (GPL) alternativel
y expressed
exon by
5/5
Y Y alternativel
y spliced
genes by RT-
90% of
Y Unknown downstream
alternative
5′ startof all
87.9%
Y Unknown (151,317)
junctions,
and 41.2%
Y Unknown None
20/20 false
N N/A positives
(FP)
validates,
175
Y** Y (18.5%) of
944 cDNA
non-intron-
2 exon
Y Y (GPL) junctions in
2 genes
Y Unknown None
Validation method
RT-PCR, qPCR, Sanger Sequencing, mRNA/EST alignments, Splicing microarrays
RT-PCR | EST and RefSeq alignments | ChIP-seq
H3K4me3 marks on alternative promoters | polyadenylation motifs supporting alternate 3' ends |
RT-PCR of novel exons followed by Sanger sequencing
EST mapping | RT-PCR
N/A
RT-PCR for FP, EST support for FN
comparison to cDNA library from same tissues: 944 events detected in cDNA librarys vs 1,602
events detected by G-Mo-R-Se = 175 events in common.
EST and gene prediction support
N/A
Performs comparisons
Visualization tool between conditions (ex.
tumor vs normal)
Extensive, includes custom graphs and links to UCSC
Y
browser
UCSC browser Y
UCSC browser N
UCSC browser N
N N
N N
Grape Genome Browser N
UCSC browser N
UCSC browser N
Practical
Relevant comparison to Alexa-seq comparison to
Alexa-seq
- -
Y Y
N N
N N
N N
N N
N N
N N
N N
Organism and
Tissue Samples
Data type supported Citation
(for publicly
available analyses
to date)
Human (37
libraries) / Mouse (4 Illumina In preparation
libraries)
Mouse myoblast cell Trapnell et al.,
line at multiple Paired-end Illumina reads 2010, Nat.
differentiation Biotech.,
timepoints 28:511-515
Guttman et al.,
Mouse ESCs, NPCs,
Illumina 2010, Nature
ATCCs
Biotech,
28:503-510 |
Au et al., 2010,
Human brain
Illumina NAR, DOI
samples (4)
10.1093/nar/gk
q211 | C,
Trapnell
Mouse brain Illumina Pachter L,
Salzberg SL.
Mouse brain, liver, 2009, et al.,
Wang
muscle; Human Illumina Plos One, 2010,
embryonic kidney Vol 5, Iss 1,
and B-cell lines e8529
Denoeud et al.,
Grape leaf, root,
Illumina 2008, Genome
stem, callus
Biol,
9(12):R175 |
Ameur et
Mouse oocytes (2) SOLiD only al.2010,
Genome Biol.,
Human UHR from Illumina | sodium bisulfite-treated DNA 11(3):R34. |
Wu and Nacu,
MAQC, simulated sequencing (for analysis of methylation 2010,
reads from genome status) Bioinformatics,
with introduced 26(7):873-881
URL
www.alexaplatform.org
http://cufflinks.cbcb.umd.edu/
http://www.broadinstitute.org/software/scripture
/
http://www.stanford.edu/group/wonglab/SpliceM
ap/
http://tophat.cbcb.umd.edu/
N/A
http://www.genoscope.cns.fr/externe/gmorse/
http://solidsoftwaretools.com/gf/project/splitseek
http://research-pub.gene.com/gmap/