EnglishFrenchSpanish

Ad


OnWorks favicon

detectChimera - Online in the Cloud

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

This is the command detectChimera 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 detectChimera online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    OfficeFloor
    OfficeFloor
    OfficeFloor provides inversion of
    coupling control, with its: - dependency
    injection - continuation injection -
    thread injection For more information
    visit the...
    Download OfficeFloor
  • 2
    DivKit
    DivKit
    DivKit is an open source Server-Driven
    UI (SDUI) framework. It allows you to
    roll out server-sourced updates to
    different app versions. Also, it can be
    used fo...
    Download DivKit
  • 3
    subconverter
    subconverter
    Utility to convert between various
    subscription format. Shadowrocket users
    should use ss, ssr or v2ray as target.
    You can add &remark= to
    Telegram-liked HT...
    Download subconverter
  • 4
    SWASH
    SWASH
    SWASH is a general-purpose numerical
    tool for simulating unsteady,
    non-hydrostatic, free-surface,
    rotational flow and transport phenomena
    in coastal waters as ...
    Download SWASH
  • 5
    VBA-M (Archived - Now on Github)
    VBA-M (Archived - Now on Github)
    Project has moved to
    https://github.com/visualboyadvance-m/visualboyadvance-m
    Features:Cheat creationsave statesmulti
    system, supports gba, gbc, gb, sgb,
    sgb2Tu...
    Download VBA-M (Archived - Now on Github)
  • 6
    Stacer
    Stacer
    Linux System Optimizer and Monitoring
    Github Repository:
    https://github.com/oguzhaninan/Stacer.
    Audience: End Users/Desktop. User
    interface: Qt. Programming La...
    Download Stacer
  • More »

Linux commands

Ad