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

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