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  • Find Splice Junction with TopHat Element

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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.Standart Illumina200
Mate standard deviationThe standard deviation for the distribution on inner distances between mate pairs. 20
Library typeSpecifies RNA-Seq protocol.FalseStandard 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.0.1False
Raw junctionsThe list of raw junctions. 
Known transcript fileA set of gene model annotations and/or known transcripts.0.15 
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.default20
Segment lengthEach read is cut up into segments, each at least this long. These segments are mapped independently.default25
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 Schema File

Type: cufflinks tophat

ParameterParameter in the GUIType
out-dirOutput directory

string

refbowtie-index-annotationdirBowtie index directorystring
rabtbowtie-index-annotationbasenameBowtie index basenamestring
librarymate-inner-typedistanceMate inner distancenumeric
maskmate-standard-filedeviationMate standard deviationstringnumeric
multilibrary-read-correcttypeLibrary typebooleannumeric
minno-isoformnovel-fractionjunctionsNo novel junctionsnumericboolean
fragraw-bias-correctjunctionsRaw junctionsstring
preknown-mrna-fractiontranscriptKnown transcript filenumericstringpath
max-multihitsMax multihitsstringnumeric
tmpsegment-dirlengthSegment lengthstringnumeric 
fusion-searchFusion search boolean
   
   
   
   
   
   
   
   
   
   
   
   
   
   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 Schema File: in-assembly

Slots:

string
Slot In GUISlot in Schema FileType
Assembly dataassemblyassembly
Source urlurlDataset namedatasetstring
Input readsfirst.inassembly
Input reads urlin-urlstring
Input paired reads urlpaired-urlstring
Input paired readssecond.inassembly

And 1 output port:

Name in GUI: Output annotations TopHat output

Name in Schema File: out-annotationsassembly

Slots:

Slot In GUISlot in Schema FileType
Isoform-level expression valuesisolevel.slotann_table Accepted hitsaccepted.hitsassembly
Accepted hits urlhits-urlstring