Difference between revisions of "ToFU2"
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$ ml tofu2 | $ ml tofu2 | ||
$ launch_tofu2 run_IceInit2.py | $ 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 18:39, 24 October 2017
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_{{#uppercase: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> ...