Question: Homer not finding any genomes?
gravatar for rf
7 days ago by
rf100 wrote:

I am creating the tagdirectories using Homer but can't get it to find the installed genome.

I am running

makeTagDirectory $tagdirname/$filename_tagDir -format HiCsummary $filename_Summary.txt -illuminaPE -removePEbg -restrictionSite GATC -genome mm10 -tbp 1

But get the error

!!! Could not find genome "mm10" !!!
    Available Genomes:
        Name    Description

        !!! No available genomes (run to load some) !!!

I have ran -install mm10 from my home folder, and the folder where the script is ran. Note that .bash_profile contains the path to /homer/bin/ and /homer/. When I ran perl -list it shows that mm10 is installed under GENOMES, and mouse-o under ORGANISMS.

Anyone help please? Thanks in advance

hic chip-seq homer • 65 views
ADD COMMENTlink modified 7 days ago • written 7 days ago by rf100

I would simply specify the path to the fasta file:

-genome <path-to-FASTA file or directory of FASTA files>
ADD REPLYlink written 7 days ago by ATpoint14k
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