Generation of average distribution profiles of ChIPseq/ATACseq/RNAseq samples around the TSS of genes.

> bin/produceTSSplots -h

SeqCode_v1.0						User commands						produceTSSplots

NAME
	produceTSSplots - a program to produce averaged ChIPseq/ATACseq/RNAseq metaplots around the TSS.

SYNOPSIS
	produceTSSplots [-bBfF <Rcolor>][-d][-g][-l <bp>][-s <reads>][-u][-w <bp>][-v][-x prefix][-h]
	<chrom_info> <refGene.txt> <SAM file> <targetGenes.txt> <name> <length>

OUTPUT
	One folder with 3 files:
	- Numerical distribution of reads.
	- R script commands.
	- Graphical representation (R is required).

OPTIONS
	-b : Background color (default: white).
	-B : General background color (default: white).
	-d : Demo mode for small BAM files (min number reads control off).
	-f : Foreground color (default: black).
	-F : General foreground color (default: black).
	-g : Generate one file with the profile of each gene.
	-l : Avg. fragment size (default: 150).
	-s : Number of spike-in reads for reference-adjusted normalization.
	-u : Generate a uniform plot with Y axis in [0-1].
	-w : Window resolution (default: 10).
	-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						produceTSSplots

Example 1. How to generate a basic ChIPseq distribution plot around the TSS of genes.

> bin/produceTSSplots -v ChromInfo.txt refGene.txt SRR1015741.bam H3K4me3_genes.txt TEST1 5000

Example 2. How to change the background and the foreground colors of the TSS plot.

> bin/produceTSSplots -v -b black -f darkgoldenrod1 ChromInfo.txt refGene.txt SRR1015741.bam H3K4me3_genes.txt TEST2 5000

Example 3. How to change the background and the foreground colors of the framebox of the TSS plot.

> bin/produceTSSplots -v -B black -F darkgoldenrod1 ChromInfo.txt refGene.txt SRR1015741.bam H3K4me3_genes.txt TEST3 5000

Example 4. How to change all the background and the foreground colors of the TSS plot.

> bin/produceTSSplots -v -B black -b black -F darkgoldenrod1 -f darkgoldenrod1 ChromInfo.txt refGene.txt SRR1015741.bam H3K4me3_genes.txt TEST4 5000

Example 5. How to generate a normalized plot in which the Y axis is between 0 and 1.

> bin/produceTSSplots -v -u ChromInfo.txt refGene.txt SRR1015741.bam H3K4me3_genes.txt TEST5 5000

Example 6. How to decrease the resolution of the picture to generate a plot with lower memory requirements.

> bin/produceTSSplots -v -w 100 ChromInfo.txt refGene.txt SRR1015741.bam H3K4me3_genes.txt TEST6 5000

Please, follow the link below for further information on how to get and preprocess the raw data of published ChIPseq and RNAseq samples utilized in this glossary of SeqCode functions.

[SAMPLES]