Homer not finding any genomes?

1

Entering edit mode

6.7 years ago

fr ▴ 220

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 configureHomer.pl to load some) !!!

I have ran configureHomer.pl -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 configureHomer.pl -list it shows that mm10 is installed under GENOMES, and mouse-o under ORGANISMS.

Anyone help please? Thanks in advance

homer hic ChIP-Seq • 4.9k views

ADD COMMENT • link 6.7 years ago by fr ▴ 220

1

Entering edit mode

I would simply specify the path to the fasta file:

-genome <path-to-FASTA file or directory of FASTA files>

ADD REPLY • link 6.7 years ago by ATpoint 90k

Login before adding your answer.