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tophat - Online in the Cloud

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This is the command tophat that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


tophat - TopHat maps short sequences from spliced transcripts to whole genomes

DESCRIPTION


tophat: TopHat maps short sequences from spliced transcripts to whole genomes.

Usage:
tophat [options] <bowtie_index> <reads1[,reads2,...]> [reads1[,reads2,...]] \
[quals1,[quals2,...]] [quals1[,quals2,...]]

OPTIONS


-v/--version

-o/--output-dir
<string> [ default: ./tophat_out ]

--bowtie1
[ default: bowtie2 ]

-N/--read-mismatches
<int> [ default: 2 ]

--read-gap-length
<int> [ default: 2 ]

--read-edit-dist
<int> [ default: 2 ]

--read-realign-edit-dist
<int> [ default: "read-edit-dist" + 1 ]

-a/--min-anchor
<int> [ default: 8 ]

-m/--splice-mismatches
<0-2> [ default: 0 ]

-i/--min-intron-length
<int> [ default: 50 ]

-I/--max-intron-length
<int> [ default: 500000 ]

-g/--max-multihits
<int> [ default: 20 ]

--suppress-hits

-x/--transcriptome-max-hits
<int> [ default: 60 ]

-M/--prefilter-multihits
( for -G/--GTF option, enable an initial bowtie search against the genome )

--max-insertion-length
<int> [ default: 3 ]

--max-deletion-length
<int> [ default: 3 ]

--solexa-quals

--solexa1.3-quals
(same as phred64-quals)

--phred64-quals
(same as solexa1.3-quals)

-Q/--quals

--integer-quals

-C/--color
(Solid - color space)

--color-out

--library-type
<string> (fr-unstranded, fr-firststrand, fr-secondstrand)

-p/--num-threads
<int> [ default: 1 ]

-R/--resume
<out_dir> ( try to resume execution )

-G/--GTF
<filename> (GTF/GFF with known transcripts)

--transcriptome-index
<bwtidx> (transcriptome bowtie index)

-T/--transcriptome-only
(map only to the transcriptome)

-j/--raw-juncs
<filename>

--insertions
<filename>

--deletions
<filename>

-r/--mate-inner-dist
<int> [ default: 50 ]

--mate-std-dev
<int> [ default: 20 ]

--no-novel-juncs

--no-novel-indels

--no-gtf-juncs

--no-coverage-search

--coverage-search

--microexon-search

--keep-tmp

--tmp-dir
<dirname> [ default: <output_dir>/tmp ]

-z/--zpacker
<program> [ default: gzip ]

-X/--unmapped-fifo
[use mkfifo to compress more temporary files for color space reads]

Advanced Options:
--report-secondary-alignments

--no-discordant

--no-mixed

--segment-mismatches
<int> [ default: 2 ]

--segment-length
<int> [ default: 25 ]

--bowtie-n
[ default: bowtie -v ]

--min-coverage-intron
<int> [ default: 50 ]

--max-coverage-intron
<int> [ default: 20000 ]

--min-segment-intron
<int> [ default: 50 ]

--max-segment-intron
<int> [ default: 500000 ]

--no-sort-bam
(Output BAM is not coordinate-sorted)

--no-convert-bam
(Do not output bam format. Output is <output_dir>/accepted_hits.sam)

--keep-fasta-order

--allow-partial-mapping

Bowtie2 related options:
Preset options in --end-to-end mode (local alignment is not used in TopHat2)

--b2-very-fast

--b2-fast

--b2-sensitive

--b2-very-sensitive

Alignment options

--b2-N
<int> [ default: 0 ]

--b2-L <int> [ default: 20 ]

--b2-i <func> [ default: S,1,1.25 ]

--b2-n-ceil
<func> [ default: L,0,0.15 ]

--b2-gbar
<int> [ default: 4 ]

Scoring options

--b2-mp
<int>,<int> [ default: 6,2 ]

--b2-np
<int> [ default: 1 ]

--b2-rdg
<int>,<int> [ default: 5,3 ]

--b2-rfg
<int>,<int> [ default: 5,3 ]

--b2-score-min
<func> [ default: L,-0.6,-0.6 ]

Effort options

--b2-D <int> [ default: 15 ]

--b2-R <int> [ default: 2 ]

Fusion related options:
--fusion-search

--fusion-anchor-length
<int> [ default: 20 ]

--fusion-min-dist
<int> [ default: 10000000 ]

--fusion-read-mismatches
<int> [ default: 2 ]

--fusion-multireads
<int> [ default: 2 ]

--fusion-multipairs
<int> [ default: 2 ]

--fusion-ignore-chromosomes
<list> [ e.g, <chrM,chrX> ]

--fusion-do-not-resolve-conflicts
[this is for test purposes ]

SAM Header Options (for embedding sequencing run metadata in output):
--rg-id
<string> (read group ID)

--rg-sample
<string> (sample ID)

--rg-library
<string> (library ID)

--rg-description
<string> (descriptive string, no tabs allowed)

--rg-platform-unit
<string> (e.g Illumina lane ID)

--rg-center
<string> (sequencing center name)

--rg-date
<string> (ISO 8601 date of the sequencing run)

--rg-platform
<string> (Sequencing platform descriptor)

for detailed help see http://tophat.cbcb.umd.edu/manual.html

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