User:Karmella Haynes/Notebook/PcTF Genomics/2013/01/07 - Revision history

Karmella Haynes: /* 01/07/13 */

2013-01-08T20:24:23Z

01/07/13

←Older revision		Revision as of 20:24, 8 January 2013
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	* Started over, but only used '''chromosomes 1-3''' as reference templates (trying a few at a time).		* Started over, but only used '''chromosomes 1-3''' as reference templates (trying a few at a time).
	** This worked		** This worked
		+

	Results/ Notes:		Results/ Notes:

Karmella Haynes: /* 01/07/13 */

2013-01-08T20:24:00Z

01/07/13

←Older revision		Revision as of 20:24, 8 January 2013
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	Results/ Notes:		Results/ Notes:
	* Peak Table: shows very few hits for PcTF, many more for H3K27me3, no overlap!		* Peak Table: shows very few hits for PcTF, many more for H3K27me3, no overlap!
-	* ~~Load the~~ wig file ~~into~~ UCSC browser online -	+	* 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

Karmella Haynes: /* 01/07/13 */

2013-01-08T20:09:15Z

01/07/13

←Older revision		Revision as of 20:09, 8 January 2013
Line 40:		Line 40:
	* Started over, but only used '''chromosomes 1-3''' as reference templates (trying a few at a time).		* Started over, but only used '''chromosomes 1-3''' as reference templates (trying a few at a time).
	** This worked		** This worked
		+
		+	Results/ Notes:
		+	* Peak Table: shows very few hits for PcTF, many more for H3K27me3, no overlap!
		+	* Load the wig file into UCSC browser online -

Karmella Haynes: /* 01/07/13 */

2013-01-08T20:00:48Z

01/07/13

←Older revision		Revision as of 20:00, 8 January 2013
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	## Configure Advanced Options: under Peak Detection, is set to Qseq Peak Finder by default. Leave this as-is for now.		## 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		## 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.


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	* Set control 2_ and 7_aln_sorted as "yes" for "Is control?"		* 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.		* 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>	+	** <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).	+	* Started over, but only used '''chromosomes 1-3''' as reference templates (trying a few at a time).
		+	** This worked

Karmella Haynes: /* 01/07/13 */

2013-01-08T17:36:22Z

01/07/13

←Older revision		Revision as of 17:36, 8 January 2013
Line 36:		Line 36:
	* Set control 2_ and 7_aln_sorted as "yes" for "Is control?"		* 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.		* 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).

Karmella Haynes: /* 01/07/13 */

2013-01-08T03:09:35Z

01/07/13

←Older revision		Revision as of 03:09, 8 January 2013
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	# Assign Binding Proteins to Experiments: Protein label = the appropriate binding protein (created in previous step). Click [Next >].		# 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.		# 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".	+	## Select "Use features of type(s)" and set to "gene".
-	#Genome filtering = Discover peaks in the entire genome.	+	## 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, 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 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.	+	## 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
		+	#

Karmella Haynes: /* 01/07/13 */

2013-01-08T03:08:03Z

01/07/13

←Older revision		Revision as of 03:08, 8 January 2013
Line 22:		Line 22:
	# Assign Binding Proteins to Experiments: Protein label = the appropriate binding protein (created in previous step). Click [Next >].		# 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.		# 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.

Karmella Haynes: /* 01/07/13 */

2013-01-08T02:41:51Z

01/07/13

←Older revision		Revision as of 02:41, 8 January 2013
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	'''PcTF vs. H3K27me3'''		'''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)	+	* 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.	+	* 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 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.	+	* Set 2_aln_sorted as control for 1_aln_sorted. Set 7_aln_sorted as control for 6_aln_sorted.

Karmella Haynes: /* 01/07/13 */

2013-01-08T02:39:33Z

01/07/13

←Older revision		Revision as of 02:39, 8 January 2013
Line 21:		Line 21:
	# 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].		# 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 >].		# 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.


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	# Set control 2_ and 7_aln_sorted as "yes" for "Is control?"		# 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.		# Set 2_aln_sorted as control for 1_aln_sorted. Set 7_aln_sorted as control for 6_aln_sorted.
		+

Karmella Haynes: /* 01/07/13 */

2013-01-08T02:35:56Z

01/07/13

←Older revision		Revision as of 02:35, 8 January 2013
Line 24:		Line 24:

	'''PcTF vs. H3K27me3'''		'''PcTF vs. H3K27me3'''
-	# Add Experiments to Import: added 6_aln_sorted.bam (H3K27me3) and ~~1_aln_sorted~~.bam (~~PcTF~~)	+	# 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.		# 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.