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

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Needed items:
* BAM file(s)
* SeqMan NGen on a Windows machine (or in parallels)
'''SeqMan workflow'''<br>
'''SeqMan workflow'''<br>
# Open SeqMan NGen
# Open SeqMan NGen
# In the Welcome window, select Import BAM file, click [Next >]
# In the Welcome window, select '''Import BAM file''', click [Next >]
# BAM Import = Align BAM layout file, click [Next >]
# BAM Import = Align BAM layout file, 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 >]
# 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 >]. <br>*Note: The template files (Homosapiens.NC_...) were downloaded from the internet using the DNASTAR QSeq application.
**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 >].<br>*Note: for this step, make sure Parallels is active, and log in as khaynes
# 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
# Your assembly is ready to begin: click [Assemble]. Wait a while.
# Your assembly is ready to begin: click [Assemble].
# The Assembly Log window and a progress bar will appear. Wait a while.


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

Revision as of 16:16, 26 June 2013

Pc-TF Genomics <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>


12/13/12

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


Needed items:

  • BAM file(s)
  • SeqMan NGen on a Windows machine (or in parallels)

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



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