Difference between revisions of "BEDTools"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
|||
| (16 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | {| | ||
| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|bedtools}} | |{{#vardefine:app|bedtools}} | ||
|{{#vardefine:url|http://code.google.com/p/bedtools/}} | |{{#vardefine:url|http://code.google.com/p/bedtools/}} | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
| Line 31: | Line 16: | ||
<!--Description--> | <!--Description--> | ||
{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
| − | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} |
| + | |||
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools. | The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools. | ||
| Line 43: | Line 29: | ||
The fact that all of the BEDTools accept input from “standard input (stdin)” allows one to “stream / pipe” several commands together to facilitate more complicated analyses. Also, the tools allow fine control over how output is reported. Most recently, I have added support for sequence alignments in BAM ([http://samtools.sourceforge.net/]) format, as well as for features in VCF and GFF, as well as “blocked” BED format. The tools are quite fast and typically finish in a matter of a few seconds, even for large datasets. | The fact that all of the BEDTools accept input from “standard input (stdin)” allows one to “stream / pipe” several commands together to facilitate more complicated analyses. Also, the tools allow fine control over how output is reported. Most recently, I have added support for sequence alignments in BAM ([http://samtools.sourceforge.net/]) format, as well as for features in VCF and GFF, as well as “blocked” BED format. The tools are quite fast and typically finish in a matter of a few seconds, even for large datasets. | ||
[http://code.google.com/p/bedtools/wiki/Usage Upstream documentation] for {{#var:app}}. | [http://code.google.com/p/bedtools/wiki/Usage Upstream documentation] for {{#var:app}}. | ||
| − | + | ||
| − | + | <!--Modules--> | |
| − | <!-- | + | ==Environment Modules== |
| − | == | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
| − | + | ==System Variables== | |
| − | < | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | |||
| − | {{ | ||
*HPC_BEDTOOLS_BIN - the bin directory | *HPC_BEDTOOLS_BIN - the bin directory | ||
*HPC_BEDTOOLS_DATA - BEDTools data directory | *HPC_BEDTOOLS_DATA - BEDTools data directory | ||
*HPC_BEDTOOLS_GENOMES - BEDTools genomes directory | *HPC_BEDTOOLS_GENOMES - BEDTools genomes directory | ||
*HPC_BEDTOOLS_SCRIPTS - BEDTools scripts directory | *HPC_BEDTOOLS_SCRIPTS - BEDTools scripts directory | ||
| + | <!--Additional--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | |||
| − | |||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 63: | Line 47: | ||
{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
Latest revision as of 12:48, 15 August 2022
Description
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools.
- Intersecting two BED files in search of overlapping features.
- Culling/refining/computing coverage for BAM alignments based on genome features.
- Merging overlapping features.
- Screening for paired-end (PE) overlaps between PE sequences and existing genomic features.
- Calculating the depth and breadth of sequence coverage across defined "windows" in a genome.
- Screening for overlaps between "split" alignments and genomic features.
The fact that all of the BEDTools accept input from “standard input (stdin)” allows one to “stream / pipe” several commands together to facilitate more complicated analyses. Also, the tools allow fine control over how output is reported. Most recently, I have added support for sequence alignments in BAM ([1]) format, as well as for features in VCF and GFF, as well as “blocked” BED format. The tools are quite fast and typically finish in a matter of a few seconds, even for large datasets. Upstream documentation for bedtools.
Environment Modules
Run module spider bedtools to find out what environment modules are available for this application.
System Variables
- HPC_BEDTOOLS_DIR - installation directory
- HPC_BEDTOOLS_BIN - the bin directory
- HPC_BEDTOOLS_DATA - BEDTools data directory
- HPC_BEDTOOLS_GENOMES - BEDTools genomes directory
- HPC_BEDTOOLS_SCRIPTS - BEDTools scripts directory