EnglishFrenchSpanish

Ad


OnWorks favicon

comparePolishes - Online in the Cloud

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

This is the command comparePolishes 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


sim4dbutils - utilities to work with sim4db-generated alignment files

convertPolishes - convert between sim4db and GFF3 formats
filterPolishes - filter alignments based on sequence identity, coverage and length.
mergePolishes - merge alignments from multiple files
sortPolishes - sort alignments by cDNA or genomic sequence index or sequence name
convertToExtent - Convert from sim4db format to a single-line tab-delimited format
fixPolishesIID - Updates a sim4db file to use the sequence index of a specific fasta file.
Can also be used to extract a subset of the alignments from the sim4db file.
depthOfPolishes - Outputs a tab-delimited histogram of the depth of polishes at various
window sizes.
headPolishes - print the first N alignments in a file, similar to head(1)
pickBestPolish - report only the 'best' alignment for each cDNA
pickUniquePolish - reports alignments where there is a clear single best alignment for
each cDNA.
plotCoverageVsIdentity - Generates (1) a histogram of the percent identity, (2) a
histogram of the percent coverage, and (3) a list of percent identity and coverage (for
use in a scatter plot).
uniqPolishes - Filters out all alignments for cDNA with multiple alignments (-uniq) or
with a single alignment (-dupl). Similar to uniq(1)
realignPolishes - recompute the alignments listed in a sim4db file.
reportAlignmentDifferences - generates a histogram of the types of errors in a set of
alignments Unsupported and Deprecated
comparePolishes - Correlate alignments in two files.
convertToAtac - Converts from sim4db format to ATAC format.
detectChimera - Examines alignments for sequences that might be chimeric.
mappedCoverage - Reports the amount of the query sequence (EST, cDNA) that is covered by
alignments.
parseSNP - Analyzes alignments for SNPs.
removeDuplicate - searches the input for duplicate alignments.
vennPolishes - Generates a Venn diagram for multiple sim4db files. Used internally by
ESTMapper cleanPolishes
summarizePolishes

DESCRIPTION


These programs are a range of utilities to work with sim4db(1)-generated alignment files.

Use comparePolishes online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    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
  • 2
    gMKVExtractGUI
    gMKVExtractGUI
    A GUI for mkvextract utility (part of
    MKVToolNix) which incorporates most (if
    not all) functionality of mkvextract and
    mkvinfo utilities. Written in C#NET 4.0,...
    Download gMKVExtractGUI
  • 3
    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
  • 4
    Frappe Books
    Frappe Books
    Frappe Books is a free and open source
    desktop book-keeping software that's
    simple and well-designed to be used by
    small businesses and freelancers. It'...
    Download Frappe Books
  • 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