User:Karmella Haynes/Notebook/PcTF Genomics/2013/01/07: Difference between revisions
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* | * Array Star analysis | ||
---- | ---- | ||
''' | '''Array Star analysis'''<br> | ||
# 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 >]. | |||
# Setup Preprocessing: Desired preprocessing = QSeq; Normalization method = none; Sequence files against which to quantify = browse to Desktop > Human Genome Ref > select all NC...gbk files. | |||
## Select "Use features of type(s)" and set to "gene". | |||
## Genome filtering = Discover peaks in the entire genome. | |||
## Configure Advanced Options: under General, Graphs > Create Wiggle (.wig). Set Location to ChIPseq Wig Files on desktop. | |||
## Configure Advanced Options: under General, Alignment Files > Create BED Alignment (.bed). Set Location to ChIPseq BED Files on desktop. | |||
## Configure Advanced Options: under Peak Detection, is set to Qseq Peak Finder by default. Leave this as-is for now. | |||
## Click [Next >]. Wait a while | |||
# Setup Attributes and Replicates: Show only grouping attributes (default). Click [Finish]. | |||
# Window with Peak Table and other tabs should appear. Finished! Explore the data. | |||
-- | |||
'''PcTF vs. H3K27me3''' | |||
* Add Experiments to Import: added 1_aln_sorted.bam (PcTF), 2_aln_sorted.bam (PcTF mock), 6_aln_sorted.bam (H3K27me3), and 7_aln_sorted.bam (H3K27me3 mock) | |||
* Create binding proteins: created "PcTF" for 1_aln_sorted, and "H3K27me3" for 6_aln_sorted. | |||
* Set control 2_ and 7_aln_sorted as "yes" for "Is control?" | |||
* Set 2_aln_sorted as control for 1_aln_sorted. Set 7_aln_sorted as control for 6_aln_sorted. | |||
** <font color="red">This analysis required too much disk space</font> | |||
* Started over, but only used '''chromosomes 1-3''' as reference templates (trying a few at a time). | |||
** This worked | |||
Results/ Notes: | |||
* Peak Table: shows very few hits for PcTF, many more for H3K27me3, no overlap! | |||
* Display wig file on UCSC Genome browser online - add file from "ChIPseq Wig Files" folder as a custom track; wig file shows raw data histogram | |||
** 1_aln_sorted.wig, 6_aln_sorted.wig | |||
* Display BED file on UCSC Genome browser online - add file from "ChIPseq BED Files" folder as a custom track; BED file shows | |||
** 1_aln_sorted.bed, 6_aln_sorted.bed | |||
Revision as of 13:24, 8 January 2013
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01/07/13
Array Star analysis
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