User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/13: Difference between revisions
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==12/13/12== | ==12/13/12== | ||
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* DNASTAR ChIP seq data analysis: SeqMan Pro | * DNASTAR ChIP seq data analysis: SeqMan NGen and SeqMan Pro | ||
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# 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). 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. | ||
# 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 15:31, 26 December 2012
 Pc-TF Genomics
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12/13/12
SeqMan workflow
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