SeqCode is designed to run under command-line platforms.
Command-line interfaces are running
environments where the user interacts with the computer by introducing text commands. SeqCode is able to
run under
Linux and
MacOSX operating systems through the command-line interface
of the Terminal (the shell). The final behavior of such programs can be configured by adding options using
the symbol '-' plus the character defining such an option. The output of the program is usually stored into
an output folder in which the user will find the resulting plots, the scripts to generate the plots in R (if any),
and the data files.
This is the prototype of a SeqCode call from the Terminal (the final format will depend on each
SeqCode program):
> SeqCode_command -options input_file1 ... input_fileN OutputFolderName
Each function of SeqCode is provided by an stand-alone program. This is the current list of available applications:
buildChIPprofile
combineChIPprofiles
combineTSSmaps
combineTSSplots
computemaxsignal
findPeaks
genomeDistribution
matchpeaks
matchpeaksgenes
processmacs
produceGENEmaps
produceGENEplots
producePEAKmaps
producePEAKplots
produceTESmaps
produceTESplots
produceTSSmaps
produceTSSplots
recoverChIPlevels
scorePhastCons
All SeqCode programs include the option '-h' to visualize the basic documentation and the full list of options to configure
it. This is an example when using this option for the buildChIPprofile command to show the help information:
> buildChIPprofile -h
SeqCode_v1.0 User commands buildChIPprofile
NAME
buildChIPprofile - a program to generate genome-wide ChIPseq/ATACseq/RNAseq profiles for genome browser visualization.
SYNOPSIS
buildChIPprofile [-c ][-d][-l ][-m][-p][-s ][-w ][-v][-x prefix][-h]
OUTPUT
One folder with one file:
- BedGraph profile (compressed).
OPTIONS
-c : Track color (default: black).
-d : Demo mode for small BAM files (min number reads control off).
-l : Avg. fragment size (default: 150).
-m : Invert the score of BedGraph records.
-p : Using pair-end reads mapped in proper pair (default: single-end).
-s : Number of spike-in reads for reference-adjusted normalization.
-w : Window resolution (default: 100).
-v : Verbose. Display info messages.
-x : Prefix for the output folder.
-h : Show this help.
SEE ALSO
SeqCode homepage: http://ldicrocelab.crg.es
GitHub source code: https://github.com/eblancoga/seqcode
AUTHORS
Written by Enrique Blanco.
SeqCode_v1.0 User commands buildChIPprofile