juicer_tools motifs with rheMac2 genome

[kquaid]

I'm getting an error when I try to use juicer_tools MotifFinder with the rheMac2 genome. Is there any place in the command line that I can specify the chrom.sizes file and the reference genome with the motifs command? (I am using the CPU version).

I've tried replacing the genomeID with the path to the chrom.sizes file, but get an ID error. If I specify the genomeID as rheMac2, I get an error saying the chrom.sizes file can't be found:

java -jar /scratch/kquaid/juicer/scripts/common/juicer_tools.jar motifs /scratch/kquaid/juicer/references/rheMac2.chrom.sizes /scratch/kquaid/novel3dte/comp_data/motifBeds/${assembly} ${dirname}/${basename}_standardized.txt -v

Unable to find proper file via VIA_ID

 Or

java -jar /scratch/kquaid/juicer/scripts/common/juicer_tools.jar motifs /scratch/kquaid/juicer/references/rheMac2.chrom.sizes /scratch/kquaid/novel3dte/comp_data/motifBeds/${assembly} ${dirname}/${basename}_standardized.txt -v

Could not find chromosome sizes file for: rheMac2

Is there a way to avoid this?  

[Muhammad Shamim]

Hi,

You'll have to pass in the chrom.sizes file, but also a list of motifs in FIMO format as we only support hg19/hg38/mm9/mm10 by default.

See the description for the custom global motif list: https://github.com/aidenlab/juicer/wiki/MotifFinder

Best,

Muhammad