EnglishFrenchSpanish

Ad


OnWorks favicon

genome-music-proximityp - Online in the Cloud

Run genome-music-proximityp in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command genome-music-proximityp 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


genome music proximity - Perform a proximity analysis on a list of mutations.

VERSION


This document describes genome music proximity version 0.04 (2016-01-01 at 23:10:18)

SYNOPSIS


genome music proximity --maf-file=? --output-file=? --output-dir=? [--max-proximity=?]
[--skip-non-coding] [--skip-silent]

... music proximity \
--maf-file input_dir/myMAF.tsv \
--output-dir output_dir/ \
--max-proximity 15

REQUIRED ARGUMENTS


maf-file Text
List of mutations using TCGA MAF specifications v2.3

output-file Text
TODO

output-dir Text
Directory where output files will be written

OPTIONAL ARGUMENTS


max-proximity Text
Maximum allowed AA distance between 2 mutations

Default value '7' if not specified

skip-non-coding Boolean
Skip non-coding mutations from the provided MAF file

Default value 'true' if not specified

noskip-non-coding Boolean
Make skip-non-coding 'false'

skip-silent Boolean
Skip silent mutations from the provided MAF file

Default value 'true' if not specified

noskip-silent Boolean
Make skip-silent 'false'

DESCRIPTION


This module first calculates the amino acid position of each mutation in the MAF file
within its respective transcript. Then, for each mutation, two values are calculated: 1)
the number of other mutations on the same transcript within the proximity limit set by the
max-proximity input parameter, and 2) the distance to the closest other mutation in this
nearby set. Only mutations which have another mutation within close proximity are reported
in the output-file.

In addition to the standard version 2.3 MAF headers, there needs to be 3 columns appended.
These column headers in the MAF must have these names in the header in order for the tool
to find them:
transcript_name - the transcript name, such as NM_000028 amino_acid_change - the amino
acid change, such as p.R290H
c_position - the nucleotide position changed, such as c.869

The output is generated with the folowing column headers: Mutations_Within_Proximity,
Nearest_Mutation, Gene, Transcript, Affected_Amino_Acid(s), Chr, Start, Stop, Ref_Allele,
Var_Allele, Sample

AUTHORS


Nathan D. Dees, Ph.D.
Dan Koboldt, M.S.
Cyriac Kandoth, Ph.D.

Use genome-music-proximityp online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    turkdevops
    turkdevops
    TurkDevOps aç?k kaynak yaz?l?m
    geli?tirici topluluklar? DevTurks-Team
    Taraf?ndan desteklenmektedir..
    Features:https://github.com/turkdevopshttps://turkdevops.g...
    Download turkdevops
  • 2
    Wine
    Wine
    Wine is an Open Source implementation
    of the Windows API on top of X and Unix.
    Wine provides both a development toolkit
    for porting Windows sources to Unix and...
    Download Wine
  • 3
    LAME (Lame Aint an MP3 Encoder)
    LAME (Lame Aint an MP3 Encoder)
    LAME is an educational tool to be used
    for learning about MP3 encoding. The
    goal of the LAME project is to improve
    the psycho acoustics, quality and speed
    of MP...
    Download LAME (Lame Aint an MP3 Encoder)
  • 4
    wxPython
    wxPython
    A set of Python extension modules that
    wrap the cross-platform GUI classes from
    wxWidgets.. Audience: Developers. User
    interface: X Window System (X11), Win32 ...
    Download wxPython
  • 5
    packfilemanager
    packfilemanager
    This is the Total War pack file manager
    project, starting from version 1.7. A
    short introduction into Warscape
    modding: ...
    Download packfilemanager
  • 6
    IPerf2
    IPerf2
    A network traffic tool for measuring
    TCP and UDP performance with metrics
    around both throughput and latency. The
    goals include maintaining an active
    iperf cod...
    Download IPerf2
  • 7
    fre:ac - free audio converter
    fre:ac - free audio converter
    fre:ac is a free audio converter and CD
    ripper for various formats and encoders.
    It features MP3, MP4/M4A, WMA, Ogg
    Vorbis, FLAC, AAC, and Bonk format
    support, ...
    Download fre:ac - free audio converter
  • More »

Linux commands

Ad