HughesLab:Protocols: Difference between revisions
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* RUM (RNA-seq Unified Mapper), is RNA-Seq alignment pipeline developed at 2011. It is freely available for academic uses. | |||
To start a job, we need to type rum_runner, give it an action telling it what to do. | |||
Actions: | |||
rum_runner align: run the RUM pipeline | |||
rum_runner clean: delete intermediate files | |||
rum_runner kill: stop running and remove all output files | |||
rum_runner stop: stop a running job | |||
rum_runner resume: resume a stopped job | |||
rum_runner status: check the status of a running job | |||
rum_runner version: print out the version of RUM | |||
rum_runner help: provide help information. | |||
Required options for rum_runner align: | |||
--index-dir, or -i: index directory | |||
--name: job_name | |||
--output or -o: output directory | |||
--chunks: number of chunks you want to | |||
forward_reads [reverse_reads] | |||
options (more details about options can be found under rum_runner help align) | |||
Required options for rum_runner help: | |||
action name | |||
Required options for Rum_runner other actions: | |||
-o | |||
Reference: | |||
1. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics. 2011 Sep 15;27(18):2518-28. | |||
2. RUM user guide. http://www.cbil.upenn.edu/RUM/userguide.php | |||
<br> | |||
<br> | |||
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[[Image:UMSL_logo.jpg|left|100px]] | [[Image:UMSL_logo.jpg|left|100px]] | ||
Revision as of 11:12, 17 February 2014
Home Lab Members Research JTK_Cycle MuscleDB Publications Protocols Academic Analytics Open Positions Contact
Molecular Biology
- Basic qPCR protocol using the ABI7900HT machine and Taqman probes: File:QPCR protocol.docx
- Arcturus RiboAmp RNA amplification from fly brains: File:RiboAmp1.docx
- Basic RT reaction using ABI Archive cDNA kit: File:RT protocol.docx
- RNA prep using Trizol and Qiagen RNeasy columns: File:RNA prep using Trizol.docx
Next-generation sequencing
- Pilot protocol for PCR amplifying fly RNA editing sites: File:Editingseq pilot.docx
Fly Behavior and Genetics
- Drosophila virgin collection: File:Drosophila virgin collection.docx
- Vials for DAM analysis: File:Fly food for DAM analysis.docx
Analytics
- Human temperature record analysis: File:Human Temp Analysis.docx
- RUM (RNA-seq Unified Mapper), is RNA-Seq alignment pipeline developed at 2011. It is freely available for academic uses.
To start a job, we need to type rum_runner, give it an action telling it what to do.
Actions:
rum_runner align: run the RUM pipeline
rum_runner clean: delete intermediate files
rum_runner kill: stop running and remove all output files
rum_runner stop: stop a running job
rum_runner resume: resume a stopped job
rum_runner status: check the status of a running job
rum_runner version: print out the version of RUM
rum_runner help: provide help information.
Required options for rum_runner align:
--index-dir, or -i: index directory
--name: job_name
--output or -o: output directory
--chunks: number of chunks you want to
forward_reads [reverse_reads]
options (more details about options can be found under rum_runner help align)
Required options for rum_runner help: action name
Required options for Rum_runner other actions: -o
Reference:
1. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics. 2011 Sep 15;27(18):2518-28.
2. RUM user guide. http://www.cbil.upenn.edu/RUM/userguide.php
Hughes Lab
Department of Biology
University of Missouri, St. Louis
