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://tophat.cbcb.umd.edu/manual.html