User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/13
From OpenWetWare
< User:Karmella Haynes | Notebook | PcTF Genomics | 2012 | 12(Difference between revisions)
(→mm/dd/yy) |
Current revision (18:31, 26 December 2012) (view source) (→12/13/12) |
||
| (12 intermediate revisions not shown.) | |||
| Line 10: | Line 10: | ||
==12/13/12== | ==12/13/12== | ||
<!-- Precede finished items with a checkmark ✓ --> | <!-- Precede finished items with a checkmark ✓ --> | ||
| - | * DNASTAR ChIP seq data analysis: SeqMan Pro | + | * DNASTAR ChIP seq data analysis: SeqMan NGen and SeqMan Pro |
| + | |||
---- | ---- | ||
| - | '''SeqMan | + | '''SeqMan workflow'''<br> |
| - | # Open SeqMan | + | # Open SeqMan NGen |
| - | # | + | # In the Welcome window, select Import BAM 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 >] | ||
| + | # 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. | ||
| + | # 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 | ||
| + | # Assembly Option: Genome ploidy = Diploid | ||
| + | # Your assembly is ready to begin: click [Assemble]. | ||
| + | # The Assembly Log window and a progress bar will appear. Wait a while. | ||
| - | Results | + | View Results |
| + | # 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 | ||
| - | # Select Contig > Strategy View | + | # Select Contig > Strategy View to view the enrichment histogram |
Current revision
 Pc-TF Genomics
|  Main project page Previous entry Next entry
|
|
12/13/12
SeqMan workflow
View Results
| |
