Oqtans Tools

tools_table

Table 1: The software packages integrated into Oqtans, with their input and output file formats. For file format abbreviations, see Table [t2]. Packages with an (a) are currently being updated. Tools for which one of the authors developed a wrapper for Galaxy integration are indicated with a (b), while tool wrappers developed by others are marked with (c). Methods that are developed by one of the authors indicated with a (d).

Name and Reference	Input	Output
Read Mapping
PALMapper[1] (b)(d)	Index, Reference Genome, FASTQ	BAM
Bowtie 1 & 2[2] (c)	Index, Reference Genome, FASTQ	SAM
BWA[3] (c)	Index, Reference Genome, FASTQ	SAM
TopHat 1 & 2[4] (c)	FASTA/Q, Index	SAM, WIG, BED
STAR[5] (b)	FASTA/Q, STAR Genome Index	BAM, BED
Gene and Transcript Prediction
Cufflinks[6] (c)	SAM/BAM, (GFF3)	GTF
mTIM[7] (a)(b)(d)	FASTA, BAM, SPF	GFF3
Scripture[8] (a)(b)	SAM/BAM	GTF
SplAdder (in preparation) (a)(b)(d)	FASTA, GFF3, BAM	GFF3
Trinity[9] (b)	FASTQ	FASTA
Quantitative Analysis
rQuant[10] (b)(d)	GFF3, BAM	GFF3
rDiff[11](b)(d)	GFF3, BAM	TAB (Gene Names)
Cuffdiff[6] (c)	SAM/BAM, (GFF3)	GTF
DESeq[12] (b)	GFF3, BAM	TAB (Gene Names)
DESeq2[12] (b)	GFF3, BAM	TAB (Gene Names)
DEXSeq[13] (b)	GFF3, BAM	TAB (Gene Names)
edgeR[14] (b)	GFF3, BAM	TAB (Gene Names)
Genesetter (b)(d)	TAB (Gene Names)	PNG, TAB (Percentages)
TopGO[15] (b)	TAB (Gene Names)	PDF
Machine Learning-based Sequence Analysis
KIRMES[16] (b)(d)	FASTA	PNG, PWM, TAB, HTML
ASP[17] (b)(d)	FASTA	GTF
ARTS[18] (a)(b)(d)	FASTA	GTF
EasySVM[19] (b)(d)	FASTA, ARFF, TAB	TAB (Classifications), PNG
Shogun[20] (b)(d)	TAB, Labels	TAB (Classifications)
Pre- and Postprocessing, File Format Utilities
GFF toolkit[21] (b)	GFF, GFF3, GTF	GFF3
SAMtools[22] (c)	SAM, BAM	SAM, BAM
RNA-geeq (manuscript in preparation) (a)(b)(d)	GFF3, BAM	BAM, TAB (Score Matrix)
WebLogo[23] (b)	PWM	PNG

Table 2: File formats used by the tools described in Table [t1] .

Extension	Stands for	Format	Used for
ARFF	Attribute-Relation File Format	Tabular	Databases
BAM	Binary SAM	Binary	Sequence alignment
BED	Browser Extensible Data	Tabular	Sequence annotation
FASTA	FAST-All	Text	Biological sequences
FASTQ	FASTA Quality	Text	Sequence reads with a quality score per base
GFF(3)	Generic Feature File (version 3)	Tabular	Sequence annotation
GTF	Gene Transfer Format	Tabular	Sequence annotation
HTML	Hypertext Markup Language	Text	Documents with text and graphics
PDF	Portable Document Format	Binary	Layouted text and image data
PNG	Portable Network Graphics	Binary	Image data
PWM	Position Weight Matrix	Tabular	Sequence motifs, e.g. binding sites
SAM	Sequence Alignment/Map	Tabular	Sequence alignment
SPF	Signal Predictor Format	Binary	Trained signal predictors from machine learning methods
TAB	Tabular Values	Tabular	Tabular data, columns separated by a character
WIG	Wiggle	Tabular	Dense continuous data

Bibliography

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RNA-seq read alignments with PALMapper.
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[2]

Langmead, B., Trapnell, C., Pop, M., and Salzberg, S. L. (2009).
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Genome Biol, 10(3).

[3]

Li, H. and Durbin, R. (2010).
Fast and accurate long-read alignment with Burrows-Wheeler transform.
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[4]

Trapnell, C., Pachter, L., and Salzberg, S. L. (2009).
TopHat: discovering splice junctions with RNA-seq.
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A. Dobin et al (2012).
STAR: ultrafast universal RNA-seq aligner.
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Roberts, A., Pimentel, H., Trapnell, C., and Pachter, L. (2011).
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Görnitz, N., Zeller, G., Behr, J., Kahles, A., Mudrakarta, P., Sonnenburg, S., and Rätsch, G. (2011).
mTiM: margin-based transcript mapping from RNA-seq.
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Full-length transcriptome assembly from rna-seq data without a reference genome.
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[10]

Bohnert, R. and Rätsch, G. (2010).
rQuant.web: a tool for RNA-seq-based transcript quantitation.
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[11]

Stegle, O., Drewe, P., Bohnert, R., Borgwardt, K., and Rätsch, G. (2010).
Statistical tests for detecting differential rna-transcript expression from read counts.
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[12]

Anders, S. and Huber, W. (2010).
Differential expression analysis for sequence count data.
Genome Biology, 11(10), R106.

[13]

Anders S, Reyes A, Huber W. (2012).
Detecting differential usage of exons from RNA-seq data.
Genome Research, 10.1101/gr.133744.111.

[14]

Robinson MD, McCarthy DJ, Smyth GK.(2010).
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Bioinformatics, 26(1):139-40.

[15]

Alexa, A., Rahnenführer, J., and Lengauer, T. (2006).
Improved scoring of functional groups from gene expression data by decorrelating go graph structure.
Bioinformatics, 22(13), 1600-1607.

[16]

Schultheiss, S. J., Busch, W., Lohmann, J. U., Kohlbacher, O., and Rätsch, G. (2009).
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.
Bioinformatics, 25(16), 2126-2133.

[17]

Sonnenburg, S., Schweikert, G., Philips, P., Behr, J., and Rätsch, G. (2007).
Accurate splice site prediction using support vector machines.
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[18]

Sonnenburg, S., Zien, A., and Rätsch, G. (2006).
Arts: accurate recognition of transcription starts in human.
Bioinformatics, 22(14), e472-80.

[19]

Ben-Hur, A., Ong, C. S., Sonnenburg, S., Schölkopf, B., and Rätsch, G. (2008).
Support vector machines and kernels for computational biology.
PLoS Comput Biol, 4(10), e1000173.

[20]

Sonnenburg, S., Rätsch, G., Henschel, S., Widmer, C., Behr, J., Zien, A., de Bona, F., Binder, A., Gehl, C., and Franc, V. (2010).
The shogun machine learning toolbox.
J Mach Learn Res, 99, 1799-1802.

[21]

Sreedharan, V. T., Behr, J., Bohnert, R., Schultheiss, S. J., and Rätsch, G. (2011).
A toolkit for pre-processing genome annotations in generic feature format.
In N. Harris and P. Rice, editors, Bioinformatics Open Source Conference, volume 12, page 47, Vienna, Austria. Open Bioinformatics Foundation.

[22]

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. (2009).
The sequence alignment/map format and samtools.
Bioinformatics, 25(16), 2078.

[23]

Crooks, G. E., Hon, G., Chandonia, J. M., and Brenner, S. E. (2004).
Weblogo: a sequence logo generator.
Genome Res, 14(6), 1188-1190.