HOMER annotation & GO

gcorre · 12-08-2014, 07:47 AM

Hi,
I have started using HOMER for peaks detection and annotation from illumina chip-seq data and it actually works well.
But when I try to provide gene expression data using the "-gene" argument or try to obtain GO informations using "-go", no additional information is parsed to the annotation file.
Does someone already experience this issues or do I make something wrong?

HOMER is running on cygwin/window7, added to $path and working well.
typical command line used :

perl annotatePeaks.pl input.bed hg19 -gene expression_data.txt or
perl annotatePeaks.pl input.bed hg19 -go /GO_output

thanks in advance,

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12-08-2014, 07:47 AM	#1
gcorre Junior Member Location: Evry Join Date: Dec 2014 Posts: 1	Hi, I have started using HOMER for peaks detection and annotation from illumina chip-seq data and it actually works well. But when I try to provide gene expression data using the "-gene" argument or try to obtain GO informations using "-go", no additional information is parsed to the annotation file. Does someone already experience this issues or do I make something wrong? HOMER is running on cygwin/window7, added to $path and working well. typical command line used : perl annotatePeaks.pl input.bed hg19 -gene expression_data.txt or perl annotatePeaks.pl input.bed hg19 -go /GO_output thanks in advance, Last edited by gcorre; 12-09-2014 at 07:18 AM.