tophat(1) 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://ccb.jhu.edu/software/tophat/manual.shtml