User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/13

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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 >]
# Set Up Project Files: Project name = some name; Project folder = SeqMan NGen Projects (desktop); Temporary file location = SeqMan NGen Projects (desktop). Click [Next >]
# 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 >].
# 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 >].
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**Note: The template files were downloaded from the internet using the DNASTAR QSeq application.
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**Note: The template files (Homosapiens.NC_...) were downloaded from the internet using the DNASTAR QSeq application.
# Input BAM Layout File: browse to Karmella's iMac > [C] Windows 7 > Users > khaynes > Desktop > ChIP seq data. Chose a .bam file. Click [Next >].
# Input BAM Layout File: browse to Karmella's iMac > [C] Windows 7 > Users > khaynes > Desktop > ChIP seq data. Chose a .bam file. Click [Next >].
# Assembly Option: Genome ploidy = Diploid
# Assembly Option: Genome ploidy = Diploid
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# Your assembly is ready to begin: click [Assemble]
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# Your assembly is ready to begin: click [Assemble. Wait a while.
View Results
View Results

Revision as of 14:42, 13 December 2012

Pc-TF Genomics Main project page
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12/13/12

  • DNASTAR ChIP seq data analysis: 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
  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.
  1. Input BAM Layout File: browse to Karmella's iMac > [C] Windows 7 > Users > khaynes > Desktop > ChIP seq data. Chose a .bam file. Click [Next >].
  2. Assembly Option: Genome ploidy = Diploid
  3. Your assembly is ready to begin: click [Assemble. Wait a while.

View Results

  1. Open SeqMan Pro
  2. Two windows appear: (1) Report, (2) filename.assembly
  3. Double click on one of the alignments in filename.assembly (e.g., NC_000001(1>249240538) NC_000001), to open "Alignment of ..." window
  4. Select Contig > Strategy View to view the enrichment histogram



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