Difference between revisions of "User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/13"

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==mm/dd/yy==
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==12/13/12==
 
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* Line item 1
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* DNASTAR ChIP seq data analysis: SeqMan NGen and SeqMan Pro
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----
 
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'''Line item 1'''<br>
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'''SeqMan workflow'''<br>
> Samples
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# Open SeqMan NGen
 
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# In the Welcome window, select Import BAM file, click [Next >]
{| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table -->
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# BAM Import = Align BAM layout file, click [Next >]
|-valign="top"
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# Set Up Project Files: Project name = some name; Project folder = SeqMan NGen Projects (desktop); Temporary file location = SeqMan NGen Projects (desktop). Click [Next >]
| <u>Reagent</u> || <u>Volume</u>  
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# Input Template Files: click [Add...]; browse to Karmella's iMac > Macintosh HD> Users > karmelahaynes > Desktop > Human Genome Ref. Select all files and click [Open]. Click [Next >]. <br>*Note: The template files (Homosapiens.NC_...) were downloaded from the internet using the DNASTAR QSeq application.
|-
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# Input BAM Layout File: browse to Karmella's iMac > '''[C] Windows 7''' > Users > khaynes > Desktop > ChIP seq data. Chose a .bam file. Click [Next >].<br>*Note: for this step, make sure Parallels is active, and log in as khaynes
| reagent 1 || # μL
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# Assembly Option: Genome ploidy = Diploid
|-
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# Your assembly is ready to begin: click [Assemble].
| reagent 2 || #
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# The Assembly Log window and a progress bar will appear. Wait a while.
|-
 
| reagent 3 || #
 
|-
 
| reagent 4 || #
 
|-
 
| dH<sub>2</sub>O || #
 
|-
 
| &nbsp; || # μL
 
|}
 
  
--> Reaction conditions
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View Results
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# Open SeqMan Pro
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# File > Open > navigate to a ###.assembly file in the SeqMan NGen Projects folder. File processing will take 10 - 15 minutes.
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# Two windows appear: (1) Report, (2) ''filename''.assembly
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# Double click on one of the alignments in ''filename''.assembly (e.g., NC_000001(1>249240538) NC_000001), to open "Alignment of ..." window
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# Select Contig > Strategy View to view the enrichment histogram
  
  

Revision as of 15:31, 26 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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12/13/12

  • DNASTAR ChIP seq data analysis: SeqMan NGen and SeqMan Pro



SeqMan workflow

  1. Open SeqMan NGen
  2. In the Welcome window, select Import BAM file, click [Next >]
  3. BAM Import = Align BAM layout file, click [Next >]
  4. Set Up Project Files: Project name = some name; Project folder = SeqMan NGen Projects (desktop); Temporary file location = SeqMan NGen Projects (desktop). Click [Next >]
  5. Input Template Files: click [Add...]; browse to Karmella's iMac > Macintosh HD> Users > karmelahaynes > Desktop > Human Genome Ref. Select all files and click [Open]. Click [Next >].
    *Note: The template files (Homosapiens.NC_...) were downloaded from the internet using the DNASTAR QSeq application.
  6. Input BAM Layout File: browse to Karmella's iMac > [C] Windows 7 > Users > khaynes > Desktop > ChIP seq data. Chose a .bam file. Click [Next >].
    *Note: for this step, make sure Parallels is active, and log in as khaynes
  7. Assembly Option: Genome ploidy = Diploid
  8. Your assembly is ready to begin: click [Assemble].
  9. The Assembly Log window and a progress bar will appear. Wait a while.

View Results

  1. Open SeqMan Pro
  2. File > Open > navigate to a ###.assembly file in the SeqMan NGen Projects folder. File processing will take 10 - 15 minutes.
  3. Two windows appear: (1) Report, (2) filename.assembly
  4. Double click on one of the alignments in filename.assembly (e.g., NC_000001(1>249240538) NC_000001), to open "Alignment of ..." window
  5. Select Contig > Strategy View to view the enrichment histogram