User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/13: Difference between revisions
From OpenWetWare
(fix raw html notebook nav) |
|||
(11 intermediate revisions by one other user not shown) | |||
Line 2: | Line 2: | ||
|- | |- | ||
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Pc-TF Genomics</span> | |style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Pc-TF Genomics</span> | ||
|style="background-color: #F2F2F2" align="center"| | |style="background-color: #F2F2F2" align="center"|[[File:Report.png|frameless|link={{#sub:{{FULLPAGENAME}}|0|-11}}]][[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|[[File:Resultset_previous.png|frameless|link={{#lnpreventry:{{FULLPAGENAME}}}}]][[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]] }}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}} | ||
|- | |- | ||
| colspan="2"| | | colspan="2"| | ||
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 | ||
---- | ---- | ||
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 | # 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) | # 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. | |||
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 |
Latest revision as of 22:19, 26 September 2017
Pc-TF Genomics | Main project page Previous entry Next entry |
12/13/12
Needed items:
SeqMan workflow
View Results
|