Evaluate the PhastCons score of a set of genomic regions.

> bin/scorePhastCons -h

SeqCode_v1.0						User commands						scorePhastCons

NAME
	scorePhastCons - a program to score genomic regions with PhastCons conservation values.

SYNOPSIS
	scorePhastCons [-t <0-1>][-w <bp>][-v][-x prefix][-h]
	<chrom_info> <refGene.txt> <PhastCons folder> <peaks.bed> <name>	

OUTPUT
	One folder with 1 file:
	- List of peaks + scores of PhastCons.

OPTIONS
	-t : Threshold to filter out predictions with PhastCons (default: 0).
	-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						scorePhastCons

Example 1. Scoring the fragments of 100 bp that constitute the region including the Nanog gene.

> bin/scorePhastCons -v ChromInfo.txt refGene.txt phastCons30way_mm9 regions.bed regions

UCSC genome browser screenshot to highlight the fragments that present at least 85% of conservation.

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]