mcool file that contains an additional normalization vector. # outdir : output directory (This should be a mounted host directory, so that the output files are visible from the host and to avoid any bus error)Īdds a normalization vector from a hic file to an mcool file. # restriction_enzyme_site_file : juicer-formatted restriction enzyme site file, each line containing a chromosome name followed by all the positions of the specific restriction enzyme sites on that chromosome, space-delimited. # reference_genome_fasta : fasta file for reference genome matching the bwaIndex # input_fastq1, input_fastq2 : input fastq files, either gzipped or not Input: a pair of fastq files, bwa Index (tgz), reference genome sequence, chrom size file and a (juicer-formatted) restriction enzyme site file.Runs juicer to create a merged_nodups file. # -n : normalization only : if this flag is used, binning is skipped. The minimun of this set must match min_res (-r). # -u custom_res : custom resolutions separated by commas (e.g. # -g : higlass-compatible : if this flag is used, zoom levels are set in a Hi-Glass compatible way, if not, default juicebox zoom levels. # -r min_res : minimum resolution for whole-genome normalization (e.g. Juice cup not included Extra-large 3 inch feed chute fits whole fruits and vegetables - Fit a whole apple, a peeled orange or a handful of kale. # -o output prefix: prefix of the output hic file Where a singleonsistent value was determined, that value is provided.1 Laboratory of Biochemistry and Food Sciences, Training and. Juicer is easy to assemble with extra-large pulp bin. # -i input_pairs : a gzipped pairs file (.pairs.gz) with its pairix index (.px2), preferably containing frag information.
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