https://github.com/gersteinlab/regulatory_targets

Scripts to identify potential target genes of regulatory elements
https://github.com/gersteinlab/regulatory_targets

Last synced: 2 months ago
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Scripts to identify potential target genes of regulatory elements

• Host: GitHub
• URL: https://github.com/gersteinlab/regulatory_targets
• Owner: gersteinlab
• Created: 2014-01-09T16:32:18.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2014-01-09T16:33:28.000Z (over 11 years ago)
• Last Synced: 2025-01-20T12:07:41.908Z (4 months ago)
• Language: C++
• Size: 5.03 MB
• Stars: 0
• Watchers: 7
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.txt

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README

        
compile: make clean 

	 make

requirement: gsl, boost regex and alglib,please alter the 'makefile' if you didn't install the boost librar in the default directory.

Usage: ./DRM2Target 

	Version: 1.07

	-b [string:required]	Bed file for DRM regions. test file: test.bed

	-g [string:required]	GTF file for gencode_v7 tss based annotation ../input_data/opt_g.gencode.v7.tss.gff

	-r [string:required]	RPM file in gff format ../input_data/opt_r.gencode.v7.tss.rpm.tsv

	-s [string:required]	Correlation significance test file is: opt_s.bed.gz ../input_data/opt_s.bed.gz

	-d [string:required]	Directory for compressed reads alignment file for methylation, H3K4me1, and H3K27ac ../bgzips/

	-l [string:required]	Meta information file for aligned data file ../input_data/opt_l.drm.meta

	-m [int:10000]      	Minimum distance between DRM and its closest gene

	-M [int:1000000]    	Maximum distance between DRM and genes,

	-p [int:0.05]       	pvalue cutoff, should be not greater than 0.05, and if '-j' is set, it is used as the adjusted pvalue cutoff for any of four adjustment methods: Bonferroni, Holm, BH and BY. Tips: if you want to output all results, please set '-p' greater than 0.05

	-j                  	Whether p-value is adjusted based on pre-calculated data. Default: not adjusted.

	-J                  	To enable '-J' will disable '-j'.  Whether p-value is adjusted within user's data. Default: not adjusted.

	-N [int: 3000]      	The maximum number of DRM regions can be suggested to run with this program. This tool only works for a small number of regions in a batch

	-c [string:1,1,1]   	Correlation methods used for methylation, H3K4me1 and H3K27ac, string delimeted by ',' with 0 and 1.[0, Pearson; 1,Spearman]

	-t [string:0,1,1]   	Tailtype for correlation significance test for methylation, H3K4me1 and H3K27ac. [0,left-tail; 1,right-tail; 2,both-tails]. When using '-j' option, use default only. Other combinations are not available for adjustment with pre-calculated data. If you want to get the raw p-value or adjustment within user's data, please don't enable '-j' option! 

	-o [string:required]	output file

	-h                  	print this help

An example:./DRM2Target -b test.bed ../input_data/opt_g.gencode.v7.tss.gff -r ../data/opt_r.gencode.v7.tss.rpm.tsv -s ../input_data/opt_s.bed.gz -d ../bgzips/ -l ../input_data/opt_l.drm.meta -o test.out