SeqCode: Program Usage

General description

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

NAME
	buildChIPprofile - a program to produce full genome ChIPseq or RNAseq profiles

SYNOPSIS
	buildChIPprofile [-c][-l][-m][-p][-s][-w][-v][-h]
	  

OUTPUT
	One folder with one file:
	- BedGraph profile (compressed)

OPTIONS
	-c : Track color (R colors)
	-l : Avg. fragment size (default: 150)
	-m: Invert the score of BedGraph records (RNAseq minus strand)
	-p: Pair-end. Using reads mapped in proper pair (default: single-end)
	-s : Number of spike-in reads (reference-adjusted normalization)
	-w : Window resolution (default: 100)
	-v: Verbose. Display info messages
	-h: Show this help

How To Access SeqCode Output

Most SeqCode commands generate one folder with the resulting output once the execution is finished. In all cases, the user must enter the name that will be used by SeqCode to generate this folder before. Those commands involving the production of PDF plots will include the final PDF file together with the R script and the data file to generate it into this folder. This is an example of the output when running the produceTSSplots command on a sample called TEST1:



Output folders of SeqCode commands that do not generate PDF plots for visualization will only include the resulting data files (e.g. BedGraph files for custom tracks or matching/mismatching peaks for intersection of peaks). This is an example of the output of the matchpeaks command on two sets called A and B:



The matchpeaksgenes command is the only one that directly delivers the results through the standard output, allowing to easily integrate this command on a pipeline to process the target genes of the analysis (the H3K4me3 ChIPseq sample in the following example):

> matchpeaksgenes -u 2500 H3K4me3_mESC.bed refGene.txt | head -10
chr1	3521328	3522342	MACS_peak_1	Xkr4	NM_001011874	chr1	-	3204562	3664079
chr1	3660177	3663163	MACS_peak_2	Xkr4	NM_001011874	chr1	-	3204562	3664079
chr1	4481311	4484482	MACS_peak_4	Sox17	NM_001289464	chr1	-	4481008	4489935
chr1	4481311	4484482	MACS_peak_4	Sox17	NM_001289465	chr1	-	4481008	4489935
chr1	4481311	4484482	MACS_peak_4	Sox17	NM_001289466	chr1	-	4481008	4489935
chr1	4481311	4484482	MACS_peak_4	Sox17	NM_001289467	chr1	-	4481008	4489935
chr1	4481311	4484482	MACS_peak_4	Sox17	NM_011441	chr1	-	4481008	4489935
chr1	4486175	4488222	MACS_peak_5	Sox17	NM_001289464	chr1	-	4481008	4489935
chr1	4486175	4488222	MACS_peak_5	Sox17	NM_001289465	chr1	-	4481008	4489935
chr1	4486175	4488222	MACS_peak_5	Sox17	NM_001289466	chr1	-	4481008	4489935

> matchpeaksgenes -u 2500 H3K4me3_mESC.bed refGene.txt | gawk '{print $5}' | sort | uniq | head -10
0610005C13Rik
0610007P14Rik
0610009B22Rik
0610009L18Rik
0610009O20Rik
0610010B08Rik
0610010F05Rik
0610010K14Rik
0610012G03Rik
0610030E20Rik