User:Karmella Haynes/Notebook/PcTF Genomics/2013/01/07

(Difference between revisions)

Revision as of 22:32, 7 January 2013

Pc-TF Genomics

Array Star analysis

Open Array Star. Windows only. This can be run on Parallels from a Mac.
Click "Start Chip-Seq project..."
Add Experiments to Import: Click [Add File..]
Select a ###.bam file from the ChiP seq data folder (shared desktop). Click [Next >].
Create binding proteins: Click [Create Binding Protein]. Binding protein label = the name of the protein that was pulled down by the antibody via ChIP. Binding site type = Unknown. Click [OK].
Assign Binding Proteins to Experiments: Protein label = the appropriate binding protein (created in previous step). Click [Next >].

PcTF vs. H3K27me3

Add Experiments to Import: added 6_aln_sorted.bam (H3K27me3) and 1_aln_sorted.bam (PcTF)
Create binding proteins: created "PcTF" for 1_aln_sorted, and "H3K27me3" for 6_aln_sorted.

@@ Line 17: / Line 17: @@
 # Open '''Array Star'''. ''Windows only. This can be run on Parallels from a Mac.''
 # Click "Start Chip-Seq project..."
-# Click [Add File..]
+# Add Experiments to Import: Click [Add File..]
 # Select a ###.bam file from the ChiP seq data folder (shared desktop). Click [Next >].
-# Create binding proteins: Click [Create Binding Protein]. Binding protein label = the name of the protein that was pulled down by the antibody via ChIP. Binding site type = Unknown.
+# Create binding proteins: Click [Create Binding Protein]. Binding protein label = the name of the protein that was pulled down by the antibody via ChIP. Binding site type = Unknown. Click [OK].
-Click [OK].
+# Assign Binding Proteins to Experiments: Protein label = the appropriate binding protein (created in previous step). Click [Next >].
+'''PcTF vs. H3K27me3'''
+# Add Experiments to Import: added 6_aln_sorted.bam (H3K27me3) and 1_aln_sorted.bam (PcTF)
+# Create binding proteins: created "PcTF" for 1_aln_sorted, and "H3K27me3" for 6_aln_sorted.