Hello all,
I am trying to run Homer's findGO.pl, and am confused as to what files I am needing for this program to run. I am working with a non-model species for what it's worth, and I think that my issues are quite basic at this point.
This is the brief description of the command:
findGO.pl <input file of Entrez Gene IDs> <organism> <output directory> [-bg <background ID file>] [-cpu #] [-human]
I am embarassingly confused at step 1! What exactly is this <input file of Entrez Gene IDs>? Is it the file I receive from, say, annotatePeaks.pl? And for <organism>, am I required to use loadGenome.pl in Homer first? I thought I had done this already, using this code:
loadGenome.pl -name perch -org null -fasta /ATACseq/FASTQ_ATAC_43955/pfluv-genome/pfluv-genome.fa -gtf /ATACseq/FASTQ_ATAC_43955/pfluv-genome/pfluv-genome.gtf
Which to my understanding should create a genome called "perch". Yet when I use "perch" for the <organism>, it does not work.
As I understand it, -bg should be used to reference the full list of genes... but I could easily be wrong.
I also have a list of all my genes, as well as a list of the human orthologs. Here is a quick example of my file:
PFLUV_G0027820 MT-ND1
PFLUV_G0027830 MT-ND2
PFLUV_G0027840 MT-CO1
PFLUV_G0027850 MT-CO2
PFLUV_G0027860 MT-ATP8
PFLUV_G0027870 MT-ATP6
PFLUV_G0027880 MT-CO3
PFLUV_G0027890 MT-ND3
PFLUV_G0027900 MT-ND4L
PFLUV_G0027910 MT-ND4
Is this type of file something I can use in this command?
Apologies for all the stupid questions, but I am very stuck and I don't see anything on the Homer website that is sufficiently answering any of my problems, so I would appreciate any insights you all might be able to provide.
Cheers,
Thanks for the input. In your opinion, do you think it would be easier to just compile a list of, say, the top 100 or so genes that pop up from Homer's annotatePeaks.pl, convert those genes to their human ortholog, and then use something like Metascape to get an analysis of that gene list? Homer's findGO.pl seems to be a really convenient tool in theory, but from where I am now it seems to not translate that well into practice.