tophat1

Tophat maps short sequences from spliced transcripts to whole genomes

Overview

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://ccb.jhu.edu/software/tophat/manual.shtml

Releases

3 releases since Debian 8 (Jessie); the text changed 2 times.