Difference between revisions of "User:Karmella Haynes/Notebook/PcTF Genomics/2012/09/21"

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'''Enrichment Histogram'''<br>
 
'''Enrichment Histogram'''<br>
 
* Start the '''Array Star''' software on the Windows platform
 
* Start the '''Array Star''' software on the Windows platform
* Open project Pc-TF (note: need to write protocol for creatign new ChIP-seq project)
+
* Open project Pc-TF (note: need to write protocol for creating new ChIP-seq project)
 
* Open the Peak Table
 
* Open the Peak Table
 
* Select rows to export
 
* Select rows to export

Revision as of 18:53, 1 December 2012

Owwnotebook icon.pngPc-TF Genomics <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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09/21/12

  • ChIP-seq: generate enrichment histogram using DNAStar "Array Star"



Enrichment Histogram

  • Start the Array Star software on the Windows platform
  • Open project Pc-TF (note: need to write protocol for creating new ChIP-seq project)
  • Open the Peak Table
  • Select rows to export
  • Choose - Data > Export
    • Save to: Browse folder (ChIP seq on desktop) and type a file name (PcTF_092112)
    • Exported Annotation Fields: click Select, choose all options
    • (✓) Export Matching Reads, check box
    • Reads Files: Browse Documents > DNASTAR > Genome > Downloads > (appropriate gbk file)
    • File format: FASTQ (with quality scores)
    • (✓) Launch NGen afterwards, check box
  • Error: Find reads mer matches. Finding matches (141 Mbases, 0.00100 k reads processed). Values exceeded storge bit allocation (Close)
  • Find new file name.gbk in ChIP seq
  • Start the Seq Man NGen software