Genome hg19**not found in homer config

JennyHu · 11-04-2015, 12:31 PM

I want to use the Homer to do annotation.
After I input "annotatePeaks.pl 31512_TH0_D0.bed hg19 > 31512_TH0_D0.ann.txt" , it shows
"!!!!Genome hg19 not found in /home/jenny/NGStools/homer/.//config.txt"

I used the command "perl /home/jenny/NGStools/homer/configureHomer.pl -install hg19" to install it, and I am sure I installed the hg19 for the homer

Then input "perl /home/jenny/NGStools/homer/configureHomer.pl -list " to
In fact, I don't know how the read the config.txt of the Homer

Can you told me why I "Genome hg19 not found " in my Homer, please?

Best,
Jenny

JennyHu · 11-04-2015, 12:44 PM

"annotatePeaks.pl /home/jenny/ATAC_Seq_FQ/macs_FQ/data/31512_TH0_D0.bed hg19 > 31512_TH0_D0.ann.txt" is wrong!

Delete the space before ">" is OK!

"annotatePeaks.pl /home/jenny/ATAC_Seq_FQ/macs_FQ/data/31512_TH0_D0.bed hg19 > 31512_TH0_D0.ann.txt"

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11-04-2015, 12:31 PM	#1
JennyHu Junior Member Location: Stanford Join Date: Nov 2015 Posts: 5	Genome hg19not found in homer config** I want to use the Homer to do annotation. After I input "annotatePeaks.pl 31512_TH0_D0.bed hg19 > 31512_TH0_D0.ann.txt" , it shows "!!!!Genome hg19 not found in /home/jenny/NGStools/homer/.//config.txt" I used the command "perl /home/jenny/NGStools/homer/configureHomer.pl -install hg19" to install it, and I am sure I installed the hg19 for the homer Then input "perl /home/jenny/NGStools/homer/configureHomer.pl -list " to In fact, I don't know how the read the config.txt of the Homer Can you told me why I "Genome hg19 not found " in my Homer, please? Best, Jenny

11-04-2015, 12:44 PM	#2
JennyHu Junior Member Location: Stanford Join Date: Nov 2015 Posts: 5	"annotatePeaks.pl /home/jenny/ATAC_Seq_FQ/macs_FQ/data/31512_TH0_D0.bed hg19 > 31512_TH0_D0.ann.txt" is wrong! Delete the space before ">" is OK! "annotatePeaks.pl /home/jenny/ATAC_Seq_FQ/macs_FQ/data/31512_TH0_D0.bed hg19 > 31512_TH0_D0.ann.txt"