Difference between revisions of "ToFU2"
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Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:Biology {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|tofu2}} |{{#vardefine:url|https://github.com/PacificBiosciences/IsoSeq_SA3nUP/wiki...") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | + | This is the developmenal (ToFU2) branch of the PacBio IsoSeq analysis | |
| − | + | software. The isoform sequencing (Iso-Seq) application generates full-length | |
| − | + | cDNA sequences — from the 5’ end of transcripts to the poly-A tail — | |
| − | + | eliminating the need for transcriptome reconstruction using | |
| − | + | isoform-inference algorithms. The Iso-Seq method generates accurate | |
| − | + | information about alternatively spliced exons and transcriptional start | |
| − | + | sites. It also delivers information about poly-adenylation sites for | |
| − | + | transcripts up to 10 kb in length across the full complement of isoforms | |
| − | + | within targeted genes or the entire transcriptome. | |
<!--Modules--> | <!--Modules--> | ||
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--> | --> | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | To launch the singularity container ToFU2 is installed in use the 'launch_tofu2' command in a [[Development_and_Testing|dev session shell]] or in a job script. E.g. | |
| − | + | $ ml tofu2 | |
| + | $ launch_tofu2 run_IceInit2.py | ||
| + | All executables from the ToFU2 install are also directly accessible after the tofu2 module is loaded. E.g. | ||
| + | $ module load tofu2 | ||
| + | $ daligner | ||
| + | <pre> | ||
| + | Usage: daligner [-vbAI] [-k<int(14)>] [-w<int(6)>] [-h<int(35)>] [-t<int>] [-M<int>] | ||
| + | [-e<double(.70)] [-l<int(1000)>] [-s<int(100)>] [-H<int>] [-T<int(4)>] | ||
| + | [-m<track>]+ <subject:db|dam> <target:db|dam> ... | ||
| + | </pre> | ||
|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
Revision as of 21:29, 6 December 2019
Description
This is the developmenal (ToFU2) branch of the PacBio IsoSeq analysis software. The isoform sequencing (Iso-Seq) application generates full-length cDNA sequences — from the 5’ end of transcripts to the poly-A tail — eliminating the need for transcriptome reconstruction using isoform-inference algorithms. The Iso-Seq method generates accurate information about alternatively spliced exons and transcriptional start sites. It also delivers information about poly-adenylation sites for transcripts up to 10 kb in length across the full complement of isoforms within targeted genes or the entire transcriptome.
Required Modules
System Variables
- HPC_TOFU2_DIR - installation directory
Additional Information
To launch the singularity container ToFU2 is installed in use the 'launch_tofu2' command in a dev session shell or in a job script. E.g.
$ ml tofu2 $ launch_tofu2 run_IceInit2.py
All executables from the ToFU2 install are also directly accessible after the tofu2 module is loaded. E.g.
$ module load tofu2 $ daligner
Usage: daligner [-vbAI] [-k<int(14)>] [-w<int(6)>] [-h<int(35)>] [-t<int>] [-M<int>]
[-e<double(.70)] [-l<int(1000)>] [-s<int(100)>] [-H<int>] [-T<int(4)>]
[-m<track>]+ <subject:db|dam> <target:db|dam> ...