QTLtools-fdensity

NAME

QTLtools fdensity - Functional density around molecular QTLs

SYNOPSIS

QTLtools fdensity --qtl significant_genes.bed --bed TFs.encode.bed.gz --out output.txt [OPTIONS]

DESCRIPTION

This mode measures the density of functional annotations around the genomic positions of molecular QTLs. The method is detailed in <https://www.nature.com/articles/ncomms15452>. In brief, we first enumerate all annotations within a given window around the molecular QTLs (by default 1âMb). Then, we split this window into small bins (default 1âkb) and count the number of functional annotations overlapping each bin. This produces an annotation count per bin that can be then plotted to see if there is any peak or depletion around the molQTLs.

OPTIONS

--qtl in.bed

List of QTLs of interest in BED format. REQUIRED.

--bed functional_annotation.bed.gz

Functional annotations in BED format. REQUIRED.

--out output.txt

Output file. REQUIRED.

--window integer

Window size around the molecular QTL position. DEFAULT=1000000

--bin integer

Bin size in base pairs. DEFAULT=1000

INPUT FILES

--qtl file

List of QTLs of interest. An example:

		1
		15210		15211		1_15211		ENSG00000227232.4			-
		1
		735984		735985		1_735985		ENSG00000177757.1			+
		1
		735984		735985		1_735985		ENSG00000240453.1			-
		1
		739527		739528		1_739528		ENSG00000237491.4			+
		The column definitions are:

--bed file

List of annotations in BED format. An example:

		1
		254874			265487
		1
		730984			735985
		1
		734984			736585
		1
		739527			748528
		The column definitions are:

OUTPUT FILE

--out file

Space separated results output file detailing the enrichment with the following columns:

EXAMPLE

	1		You need to prepare a BED file containing the positions of the QTLs of interest. To do so, extract all significant hits at a given FDR threshold (e.g. 5%), and then transform the significant QTL list into a BED file:
			Rscript ./script/qtltools_runFDR_cis.R results.genes.full.txt.gz 0.05 results.genes

cat results.genes.significant.txt | awk ’{ print $9, $10-1, $11, $8, $1, $5 }’ | tr ’ ’ ’\t’ | sort -k1,1V -k2,2g > results.genes.significant.bed

	2		Measure the density using the following command:
			QTLtools fdensity --qtl results.genes.significant.bed --bed TFs.encode.bed.gz --out density.TF.around.QTL.txt

SEE ALSO

QTLtools(1)

QTLtools website: <https://qtltools.github.io/qtltools>

BUGS

Please submit bugs to <https://github.com/qtltools/qtltools>

CITATION

Delaneau, O., Ongen, H., Brown, A. et al. A complete tool set for molecular QTL discovery and analysis. Nat Commun 8, 15452 (2017). <https://doi.org/10.1038/ncomms15452>

AUTHORS

Olivier Delaneau (olivier.delaneau@gmail.com), Halit Ongen (halitongen@gmail.com)