Difference between revisions of "Juicer"
(Created page with "Category:SoftwareCategory:BiologyCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|juicer}} |{{#vardefine:url|https://github.com/theaidenla...") |
|||
| (4 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|juicer}} | |{{#vardefine:app|juicer}} | ||
| Line 18: | Line 18: | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps. | + | Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps. The juicer pipeline submits jobs to the cluster and then exits. It can therefore be run on the login node. Individual tools (see $HPC_JUICER_DIR/scripts) can be run as batch jobs or interactively. Type "juicer.sh -h" to see options and help menu. |
| + | |||
| + | Juicer depends on reference files (bwa index plus chromosome sizes file) and restriction enzyme files that are part of the central install. You can build additional references yourself or ask UFRC staff to generate them centrally. See $HPC_JUICER_DIR/references and $HPC_JUICER_DIR/restriction_sites for available reference data. | ||
<!--Modules--> | <!--Modules--> | ||
| Line 24: | Line 26: | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 16:29, 15 October 2023
Description
Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps. The juicer pipeline submits jobs to the cluster and then exits. It can therefore be run on the login node. Individual tools (see $HPC_JUICER_DIR/scripts) can be run as batch jobs or interactively. Type "juicer.sh -h" to see options and help menu.
Juicer depends on reference files (bwa index plus chromosome sizes file) and restriction enzyme files that are part of the central install. You can build additional references yourself or ask UFRC staff to generate them centrally. See $HPC_JUICER_DIR/references and $HPC_JUICER_DIR/restriction_sites for available reference data.
Environment Modules
Run module spider juicer to find out what environment modules are available for this application.
System Variables
- HPC_JUICER_DIR - installation directory
- HPC_JUICER_BIN - executable directory