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Old 11-04-2015, 12:31 PM   #1
JennyHu
Junior Member
 
Location: Stanford

Join Date: Nov 2015
Posts: 5
Red face Genome hg19**not 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
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Old 11-04-2015, 12:44 PM   #2
JennyHu
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Location: Stanford

Join Date: Nov 2015
Posts: 5
Default

"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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