HughesLab:Protocols: Difference between revisions

Revision as of 11:15, 17 February 2014

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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

Pilot protocol for PCR amplifying fly RNA editing sites: File:Editingseq pilot.docx

Hughes Lab
Department of Biology
University of Missouri, St. Louis

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+* RUM (RNA-Seq Unified Mapper) guide: [[Image:RUM_guide]]
-* 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:
-. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics. 2011 Sep 15;27(18):2518-28.
-. RUM user guide. http://www.cbil.upenn.edu/RUM/userguide.php
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