User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/26: Difference between revisions

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Workflow
Workflow
* Open SeqMan Pro. File > Open > navigate to the desired ###.assmebly file in the SeqMan NGen Projects folder. Processing takes 5 -10 minutes.
* Open SeqMan Pro. ''File > Open >'' ...navigate to the desired ###.assembly file in the SeqMan NGen Projects folder. Processing takes 5 -10 minutes.
* In an internet browser, go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.
* In an internet browser, go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.
* Enter a gene name. Click [Submit].  
* Enter a gene name. Click [Submit].  
* Take note of the chromosome number and coordinates.
* Take note of the chromosome number and coordinates.
* Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.
* Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.
* Select ''Contig > Strategy View'' to view the enrichment histogram




Revision as of 15:53, 26 December 2012

Pc-TF Genomics <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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12/26/12

  • ChIP-seq enrichment: PcTF vs. PcTF mock for select genes

ChIP: PcTF vs. PcTF mock

  • Completed PcTF (lane 1) and PcTF mock (lane 2) BAM --> assembly workflow
  • Open in SeqMan pro to see raw values for four genes from 2011 paper.


Workflow

  • Open SeqMan Pro. File > Open > ...navigate to the desired ###.assembly file in the SeqMan NGen Projects folder. Processing takes 5 -10 minutes.
  • In an internet browser, go to the UCSC genome browser. Select Feb. 2009 GRCh37/hg19.
  • Enter a gene name. Click [Submit].
  • Take note of the chromosome number and coordinates.
  • Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.
  • Select Contig > Strategy View to view the enrichment histogram


1. Name: CDKN2A, Coordinates: chr9: 21,967, 751..21,975,132

  • SeqMan Pro template "NC000009(1>141215022) NC_000009"




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