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

(Difference between revisions)

Revision as of 15:41, 13 December 2012

Pc-TF Genomics

SeqMan workflow

Open SeqMan NGen
In the Welcome window, select Import BAM file, click [Next >]
BAM Import = Align BAM layout file
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 >].

- Note: The template files 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 >].
Assembly Option: Genome ploidy = Diploid
Your assembly is ready to begin: click [Assemble]

View Results

Open SeqMan Pro
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
Select Contig > Strategy View to view the enrichment histogram

@@ Line 20: / Line 20: @@
 # 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 were downloaded from the internet using the DNASTAR QSeq application.
-# Input BAM Layout File: browse to
+# 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
+# Your assembly is ready to begin: click [Assemble]
 View Results