File	Date	Author	Commit
README	2013-02-21	Chaolin Zhang	[10e54e] Initial release to the public
bedUniq.pl	2013-02-21	Chaolin Zhang	[10e54e] Initial release to the public
combineTranscripts.pl	2013-02-21	Chaolin Zhang	[10e54e] Initial release to the public
gene2ExonIntron.pl	2013-02-21	Chaolin Zhang	[10e54e] Initial release to the public
tag2peak.pl	2013-02-21	Chaolin Zhang	[10e54e] Initial release to the public
tag2profile.pl	2013-02-21	Chaolin Zhang	[10e54e] Initial release to the public
tagoverlap.pl	2013-02-21	Chaolin Zhang	[10e54e] Initial release to the public

Read Me

A typical command line:

perl ~/path/to/dir/tag2peak.pl -ss --multi-test -v gene.in.bed tag.in.bed peak.out.bed

gene.in.bed is the gene annotation file. tag.in.bed is the CLIP tag file.

If you do not want to distinguish exons and introns, provide a gene.in.bed file with the first 6 columns. Otherwise, provide a 12-column BED file with additional information of exon/intron structure.

If your tag.in.bed file is large (e.g., > 6M tags), run with an additional option -big

If you want to normalize by gene expression level, provide the abundance (linear scale) in the score (5th) column gene.in.bed file.