DOKK / manpages / debian 10 / tophat / tophat.1.en
TOPHAT(1) User Commands TOPHAT(1)

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

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

[quals1,[quals2,...]] [quals1[,quals2,...]]

-v/--version

<string> [ default: ./tophat_out ]
[ default: bowtie2 ]
<int> [ default: 2 ]
<int> [ default: 2 ]
<int> [ default: 2 ]
<int> [ default: "read-edit-dist" + 1 ]
<int> [ default: 8 ]
<0-2> [ default: 0 ]
<int> [ default: 50 ]
<int> [ default: 500000 ]
<int> [ default: 20 ]

--suppress-hits

<int> [ default: 60 ]
( for -G/--GTF option, enable an initial bowtie search against the genome )
<int> [ default: 3 ]
<int> [ default: 3 ]

--solexa-quals

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

-Q/--quals

--integer-quals

(Solid - color space)

--color-out

<string> (fr-unstranded, fr-firststrand, fr-secondstrand)
<int> [ default: 1 ]
<out_dir> ( try to resume execution )
<filename> (GTF/GFF with known transcripts)
<bwtidx> (transcriptome bowtie index)
(map only to the transcriptome)
<filename>
<filename>
<filename>
<int> [ default: 50 ]
<int> [ default: 20 ]

--no-novel-juncs

--no-novel-indels

--no-gtf-juncs

--no-coverage-search

--coverage-search

--microexon-search

--keep-tmp

<dirname> [ default: <output_dir>/tmp ]
<program> [ default: gzip ]
[use mkfifo to compress more temporary files for color space reads]

--report-secondary-alignments

--no-discordant

--no-mixed

<int> [ default: 2 ]
<int> [ default: 25 ]
[ default: bowtie -v ]
<int> [ default: 50 ]
<int> [ default: 20000 ]
<int> [ default: 50 ]
<int> [ default: 500000 ]
(Output BAM is not coordinate-sorted)
(Do not output bam format. Output is <output_dir>/accepted_hits.sam)

--keep-fasta-order

--allow-partial-mapping

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
<int> [ default: 0 ]
<int> [ default: 20 ]
<func> [ default: S,1,1.25 ]
<func> [ default: L,0,0.15 ]
<int> [ default: 4 ]
Scoring options
<int>,<int> [ default: 6,2 ]
<int> [ default: 1 ]
<int>,<int> [ default: 5,3 ]
<int>,<int> [ default: 5,3 ]
<func> [ default: L,-0.6,-0.6 ]
Effort options
<int> [ default: 15 ]
<int> [ default: 2 ]

--fusion-search

<int> [ default: 20 ]
<int> [ default: 10000000 ]
<int> [ default: 2 ]
<int> [ default: 2 ]
<int> [ default: 2 ]
<list> [ e.g, <chrM,chrX> ]
[this is for test purposes ]

<string> (read group ID)
<string> (sample ID)
<string> (library ID)
<string> (descriptive string, no tabs allowed)
<string> (e.g Illumina lane ID)
<string> (sequencing center name)
<string> (ISO 8601 date of the sequencing run)
<string> (Sequencing platform descriptor)
for detailed help see http://ccb.jhu.edu/software/tophat/manual.shtml
November 2018 tophat 2.1.1+dfsg1-2+b1