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