EnglishFrenchSpanish

Ad


OnWorks favicon

bed2gff3p - Online in the Cloud

Run bed2gff3p in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command bed2gff3p that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


ucsc_genes2gff.pl - Convert UCSC Genome Browser-format gene files into GFF files suitable
for loading into gbrowse

SYNOPSIS


% uscsc_genes2gff.pl [options] ucsc_file1 ucsc_file2...

Options:

-src <string> Choose a source for the gene, default "UCSC"
-origin <integer> Choose a relative position to number from, default
is "1"

DESCRIPTION


This script massages the gene files available from the "tables" link of the UCSC genome
browser (genome.ucsc.edu) into a form suitable for loading of gbrowse. Warning: it only
works with the gene tables. Other tables, such as EST alignments, contours and repeats,
have their own formats which will require other scripts to parse.

To use this script, get one or more UCSC tables, either from the "Tables" link on the
browser, or from the UCSC Genome Browser FTP site. Give the table file as the argument to
this script. You may want to provide an alternative "source" field. Otherwise this
script defaults to "UCSC".

% pucsc_genes2gff.pl -src RefSeq refseq_data.ucsc > refseq.gff

The resulting GFF file can then be loaded into a Bio::DB::GFF database using the following
command:

% bulk_load_gff.pl -d <databasename> refseq.gff

Use bed2gff3p online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    OpenFOAM
    OpenFOAM
    OpenFOAM - The Open Source CFD Toolbox.
    OpenFOAM is a generic, programmable
    software tool for Computational Fluid
    Dynamics (CFD). For more information,
    see: - ...
    Download OpenFOAM
  • 2
    PostInstallerF
    PostInstallerF
    PostInstallerF will install all the
    software that Fedora Linux and others
    doesn't include by default, after
    running Fedora for the first time. Its
    easy for...
    Download PostInstallerF
  • 3
    strace
    strace
    The strace project has been moved to
    https://strace.io. strace is a
    diagnostic, debugging and instructional
    userspace tracer for Linux. It is used
    to monitor a...
    Download strace
  • 4
    JasperReports Library
    JasperReports Library
    JasperReports Library is the
    world's most popular open source
    business intelligence and reporting
    engine. It is entirely written in Java
    and it is able to ...
    Download JasperReports Library
  • 5
    Numerical Python
    Numerical Python
    NEWS: NumPy 1.11.2 is the last release
    that will be made on sourceforge. Wheels
    for Windows, Mac, and Linux as well as
    archived source distributions can be fou...
    Download Numerical Python
  • 6
    CMU Sphinx
    CMU Sphinx
    CMUSphinx is a speaker-independent large
    vocabulary continuous speech recognizer
    released under BSD style license. It is
    also a collection of open source tools ...
    Download CMU Sphinx
  • 7
    Old Feren OS Repositories
    Old Feren OS Repositories
    This was the Official Repository for
    Feren OS. To add the latest one, run
    this command: (16.04-based) echo
    "deb ...
    Download Old Feren OS Repositories
  • More »

Linux commands

Ad