EnglishFrenchSpanish

OnWorks favicon

fastq-multx - Online in the Cloud

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

This is the command fastq-multx 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


fastq-multx - ea-utils: replace % with the barcode id in the barcodes file

SYNOPSIS


fastq-multx [-g|-l|-B] <barcodes.fil> <read1.fq> -o r1.%.fq [mate.fq -o r2.%.fq] ...

DESCRIPTION


fastq-multx: invalid option -- 'h' Unknown option `-h'.

Version: 1.02.684

Output files must contain a '%' sign which is replaced with the barcode id in the barcodes
file. Output file can be n/a to discard the corresponding data (use this for the barcode
read)

Barcodes file (-B) looks like this:

<id1> <sequence1> <id2> <sequence2> ...

Default is to guess the -bol or -eol based on clear stats.

If -g is used, then it's parameter is an index lane, and frequently occuring sequences are
used.

If -l is used then all barcodes in the file are tried, and the *group* with the *most*
matches is chosen.

Grouped barcodes file (-l or -L) looks like this:

<id1> <sequence1> <group1> <id1> <sequence1> <group1> <id2> <sequence2> <group2>...

Mated reads, if supplied, are kept in-sync

OPTIONS


-o FIL1 Output files (one per input, required) -g SEQFIL Determine barcodes from
indexed read SEQFIL -l BCFIL Determine barcodes from any read, using BCFIL as a master
list -L BCFIL Determine barcodes from <read1.fq>, using BCFIL as a master list -B BCFIL
Use barcodes from the specified file, don't run a determination step -b Force
beginning of line (5') for barcode matching -e Force end of line (3') for batcode
matching -t NUM Divide threshold for auto-determine by factor NUM (1), > 1 = more
sensitive -G NAME Use group(s) matching NAME only -x Don't trim barcodes off
before writing out destination -n Don't execute, just print likely barcode list
-v C Verify that mated id's match up to character C (Use ' ' for illumina) -m N
Allow up to N mismatches, as long as they are unique (1) -d N Require a minimum
distance of N between the best and next best (2) -q N Require a minimum phred
quality of N to accept a barcode base (0)

Use fastq-multx online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Image Downloader
    Image Downloader
    Crawl and download images using
    Selenium Using python3 and PyQt5.
    Supported Search Engine: Google, Bing,
    Baidu. Keywords input from the keyboard
    or input from ...
    Download Image Downloader
  • 2
    Eclipse Tomcat Plugin
    Eclipse Tomcat Plugin
    The Eclipse Tomcat Plugin provides
    simple integration of a tomcat servlet
    container for the development of java
    web applications. You can join us for
    discussio...
    Download Eclipse Tomcat Plugin
  • 3
    WebTorrent Desktop
    WebTorrent Desktop
    WebTorrent Desktop is for streaming
    torrents on Mac, Windows or Linux. It
    connects to both BitTorrent and
    WebTorrent peers. Now there's no
    need to wait for...
    Download WebTorrent Desktop
  • 4
    GenX
    GenX
    GenX is a scientific program to refine
    x-ray refelcetivity, neutron
    reflectivity and surface x-ray
    diffraction data using the differential
    evolution algorithm....
    Download GenX
  • 5
    pspp4windows
    pspp4windows
    PSPP is a program for statistical
    analysis of sampled data. It is a free
    replacement for the proprietary program
    SPSS. PSPP has both text-based and
    graphical us...
    Download pspp4windows
  • 6
    Git Extensions
    Git Extensions
    Git Extensions is a standalone UI tool
    for managing Git repositories. It also
    integrates with Windows Explorer and
    Microsoft Visual Studio
    (2015/2017/2019). Th...
    Download Git Extensions
  • More »

Linux commands

Ad