Provided by: tophat_2.0.9-1ubuntu1_amd64
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_hit.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