---
name: "tophat"
section: "1"
platform: "linux"
package: "tophat"
version: "2.1.1+dfsg1-2+b1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/tophat"
---

# tophat(1)

TopHat maps short sequences from spliced transcripts to whole genomes

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