SeqCode: scorePhastCons

General description

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

Examples

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.

ChIPseq and RNAseq samples

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]