TopHat-Teaching

Category

Bioinformatics

Program On

Teaching

Version

2.1.1

Author / Distributor

TopHat

Description

"TopHat is a fast splice junction mapper for RNA-Seq reads." More details are at TopHat

Running Program

The last version of this application is at /usr/local/apps/eb/TopHat/2.1.1-foss-2016b

To use this version, please load the module with

ml TopHat/2.1.1-foss-2016b 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_TopHat
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=TopHat.%j.out

cd $SLURM_SUBMIT_DIR
ml TopHat/2.1.1-foss-2016b
tophat [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml TopHat/2.1.1-foss-2016b 
tophat tophat --help
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

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Installation

Source code is obtained from TopHat

System

64-bit Linux