UseFurtherInfo

Introduction

ngs.plot now contains a database of thousands of tables across multiple species, gene types and regions. This makes it difficult for a user to find the genomic regions for plot. To avoid cluttering the command line interface, we design a mechanism for users to select tables based on a single string of descriptors that are separated by comma. This keeps the command line concise while remains the flexibility.

Usage

Briefly, the -F option should be followed by a string of descriptors like this:

-F [gene_type][,sub_region][,cell_line or tissue][,exon_type][,rnaseq or chipseq]

Please be advised that the option to switch between chip-seq and rna-seq plots can also be provided here. You don't have to give all the descriptors. One descriptor or three descriptors work just fine. When a certain variable is not specified, ngs.plot chooses the default values. For example,

-G hg19 -R enhancer -F K562

will select the enhancers in the K562 cell line for protein coding genes, although protein_coding is not specified here. The order of the descriptors does not matter, that means

-F protein_coding,K562

and

-F K562,protein_coding

are the same. Do NOT feel nervous for making typos or inputting wrong combinations. ngs.plot will always choose a default table if some descriptions do not match the database. The actual database table being used will be given on the command console for your reference.

Descriptors

Here are the available values you can use in ngs.plot:

Gene Type

protein_coding(default)	pseudogene	lincRNA	miRNA	misc(everything else)

Exon Type

canonical(default)	altAcceptor	altBoth	altDonor	polyA	promoter	variant

CGI & DHS classification

ProximalPromoter(default)	Promoter1k	Promoter3k	Genebody	Genedesert	OtherIntergenic	Pericentromere	Subtelomere

Human cell line

dhs

H1hesc(default)	A549	Gm12878	Helas3	Hepg2	Hmec	Hsmm	Hsmmtube	Huvec	K562	Lncap	Mcf7	Nhek	Th1

enhancer

H1hesc(default)	Gm12878	Hepg2	Hmec	Hsmm	Huvec	K562	Nhek	Nhlf

Mouse tissue (enhancer only)

mESC(default)	boneMarrow	cerebellum	cortex	heart	intestine	kidney	liver	lung	MEF	olfactoryBulb	placenta	spleen	testes	thymus