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TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

Parameters in GUI

ParameterDescriptionDefault value
Output directoryDirectory to save MACS output files. 
Bowtie index directoryThe directory with the Bowtie index for the reference sequence. 
Bowtie index basenameThe basename of the Bowtie index for the reference sequence. 
Mate inner distanceThe expected (mean) inner distance between mate pairs.200
Mate standard deviationThe standard deviation for the distribution on inner distances between mate pairs.20
Library typeSpecifies RNA-Seq protocol.Standard Illumins
No novel junctionsOnly look for reads across junctions indicated in the supplied GFF or junctions file. This parameter is ignored if Raw junctions or Known transcript file is not set.False
Raw junctionsThe list of raw junctions. 
Known transcript fileA set of gene model annotations and/or known transcripts. 
Max multihitsInstructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many alignments.20
Segment lengthEach read is cut up into segments, each at least this long. These segments are mapped independently.25
Fusion searchTurn on fusion mapping.False
Transcriptome onlyOnly align the reads to the transcriptome and report only those mappings as genomic mappings.False
Transcriptome max hitsMaximum number of mappings allowed for a read, when aligned to the transcriptome (any reads found with more than this number of mappings will be discarded).60
Prefilter multihitsWhen mapping reads on the transcriptome, some repetitive or low complexity reads that would be discarded in the context of the genome may appear to align to the transcript sequences and thus may end up reported as mapped to those genes only. This option directs TopHat to first align the reads to the whole genome in order to determine and exclude such multi-mapped reads (according to the value of the Max multihits option).False
Min anchor lengthThe anchor length. TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one read with this many bases on each side.8
Splice mismatchesThe maximum number of mismatches that may appear in the anchor region of a spliced alignment.0
Read mismatchesFinal read alignments having more than these many mismatches are discarded.2
Segment mismatchesRead segments are mapped independently, allowing up to this many mismatches in each segment alignment.2
Solexa 1.3 qualsAs of the Illumina GA pipeline version 1.3, quality scores are encoded in Phred-scaled base-64. Use this option for FASTQ files from pipeline 1.3 or later.False
Bowtie versionSpecifies which Bowtie version should be used.Bowtie2
Bowtie -n modeTopHat uses -v in Bowtie for initial read mapping (the default), but with this option, -n is used instead. Read segments are always mapped using -v option.Use -v mode
Bowtie tool pathThe path to the Bowtie external tool.default
SAMtools tool pathThe path to the SAMtools tool. Note that the tool is available in the UGENE External Tool Package.default
TopHat tool pathThe path to the TopHat external tool in UGENE.default
Temporary directoryThe directory for temporary files.default

Parameters in Workflow File

Type: tophat

ParameterParameter in the GUIType
out-dirOutput directory


bowtie-index-dirBowtie index directorystring
bowtie-index-basenameBowtie index basenamestring
mate-inner-distanceMate inner distancenumeric
mate-standard-deviationMate standard deviationnumeric
library-typeLibrary typenumeric
no-novel-junctionsNo novel junctionsboolean
raw-junctionsRaw junctionsstring
known-transcriptKnown transcript filestring
max-multihitsMax multihitsnumeric
segment-lengthSegment lengthnumeric
fusion-searchFusion searchboolean
transcriptome-onlyTranscriptome onlyboolean
transcriptome-max-hitsTranscriptome max hitsnumeric
prefilter-multihitsPrefilter multihitsboolean
min-anchor-lengthMin anchor lengthnumeric
splice-mismatchesSplice mismatchesnumeric
read-mismatchesRead mismatchesnumeric
segment-mismatchesSegment mismatchesnumeric
solexa-1-3-qualsSolexa 1.3 qualsboolean
bowtie-versionBowtie versionnumeric
bowtie-n-modeBowtie -n modenumeric
bowtie-tool-pathBowtie tool pathstring
samtools-tool-pathSAMtools tool pathstring
pathTopHat tool pathstring
temp-dirTemporary directorystring

Input/Output Ports

The element has 1 input port:

Name in GUI: Input reads

Name in Workflow File: in-assembly


Slot In GUISlot in Workflow FileType
Dataset namedatasetstring
Input readsfirst.inassembly
Input reads urlin-urlstring
Input paired reads urlpaired-urlstring
Input paired readssecond.inassembly

And 1 output port:

Name in GUI: TopHat output

Name in Workflow File: out-assembly


Slot In GUISlot in Workflow FileType
Accepted hitsaccepted.hitsassembly
Accepted hits urlhits-urlstring
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