February 2, 2016 - Revision history

Asgruber: /* R-Commander Work */

2016-03-08T15:21:53Z

‎R-Commander Work

Asgruber at 15:20, 8 March 2016

2016-03-08T15:20:52Z

Asgruber at 17:22, 13 February 2016

2016-02-13T17:22:34Z

Asgruber: /* Classwork */

2016-02-13T17:22:14Z

‎Classwork

Asgruber: /* Classwork */

2016-02-13T17:15:25Z

‎Classwork

Asgruber: /* Classwork */

2016-02-13T17:14:06Z

‎Classwork

Asgruber: /* Classwork */

2016-02-13T17:13:36Z

‎Classwork

Asgruber: /* Classwork */

2016-02-13T17:12:40Z

‎Classwork

Asgruber at 17:11, 13 February 2016

2016-02-13T17:11:02Z

Asgruber at 17:01, 13 February 2016

2016-02-13T17:01:29Z

@@ Line 35: / Line 35: @@
 === R-Commander Work ===
-*Compare gene out put for all of liver reads to all of intestine reads.
+*Compare gene output for all of liver reads to all of intestine reads.
 *Generate heat map (FIGURE OUT HOW TO ADD SCREENSHOT).
 **Liver and intestine are expressing different genes.
@@ Line 45: / Line 45: @@
 '''''Moving forward, we need to figure out the codes that will allow us to cluster genes in the most logical way.''''''
-*Intestines Group 3 is trying to write code to cluster only intestines data for the 3 fed versus the 3 non-fed snakes.
+*Intestines Group 3 is trying to write a code to cluster only intestines data for the 3 fed versus the 3 non-fed snakes.

← Older revision		Revision as of 15:20, 8 March 2016
Line 26:		Line 26:


−	'''''Moving forward, we need to assign gene ontology terms to all genes.''''''	+	'''''Moving forward, we need to assign gene ontology terms to all genes.'''''

@@ Line 1: / Line 1: @@
 == Classwork ==
-'=== Today in class, we shared group findings from [[January 28, 2016]]: ===
+=== Today in class, we shared group findings from [[January 28, 2016]]: ===
 . Blast the overrepresented sequences
@@ Line 27: / Line 27: @@
 '''''Moving forward, we need to assign gene ontology terms to all genes.''''''
 == DEseq ==

@@ Line 1: / Line 1: @@
 == Classwork ==
-'''Today in class, we shared group findings from [[January 28, 2016]]:'''
+'=== Today in class, we shared group findings from [[January 28, 2016]]: ===
 . Blast the overrepresented sequences
@@ Line 25: / Line 25: @@
 *Data can be normalized using a total read count (TC) normalization.

← Older revision		Revision as of 17:15, 13 February 2016
Line 30:		Line 30:


		+	[http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Ashlyn Ashlyn's Main Page]



−	[http://~~gcat~~.davidson.edu/~~mediawiki-1~~.19.~~1/index.php/Ashlyn Ashlyn's Main Page~~]	+
		+
		+	<big>''References"</big>
		+
		+	*Andrew, Audra L., et al. “Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding.” Physiol Genomics. 47 (2015): 147-157.
		+	:::[http://www.bio.davidson.edu/Courses/Bio343/2016/4a_Todd%20Castoe%20Python%20RNAseq_2015.pdf Andrew et al. (2015)]

@@ Line 2: / Line 2: @@
 '''Today in class, we shared group findings from [[January 28, 2016]]:'''
-#Blast the overrepresented sequences
+. Blast the overrepresented sequences
-##Blast groups found mostly mitochondrial or ribosomal genes.
+*Blast groups found mostly mitochondrial or ribosomal genes.
-##Intestine blast group found an amino transferase gene that may be of interest later.
+*Intestine blast group found an amino transferase gene that may be of interest later.
-##Liver blast group found an anti-hemorage gene that may be of interest later.
+*Liver blast group found an anti-hemorage gene that may be of interest later.
-#Attempt to access the list of genes (SRP-0151827) mentioned in the Andrew et al. (2015) study
+. Attempt to access the list of genes (SRP-0151827) mentioned in the Andrew et al. (2015) study
-##We can blast our sequences against the Andrew et al. (2015) library.
+*We can blast our sequences against the Andrew et al. (2015) library.
-##We have the potential to download the entire library with instructions on the website, but do not understand how to use the software/programs required to do so.
+*We have the potential to download the entire library with instructions on the website, but do not understand how to use the software/programs required to do so.
-##We found a toolkit that allows us to download one sequence at a time.
+*We found a toolkit that allows us to download one sequence at a time.
-##We can blast within a run.
+*We can blast within a run.
-#Add numbers to label proteins of "unknown function" in our reads
+. Add numbers to label proteins of "unknown function" in our reads
-##Dylan and Dustin made a file that removed duplicate names from our runs.
+*Dylan and Dustin made a file that removed duplicate names from our runs.
-##Dr. Campbell and Dr. Heyer used their file and got gene mapping results!
+*Dr. Campbell and Dr. Heyer used their file and got gene mapping results!
-#Normalize relative abundance of transcripts
+.Normalize relative abundance of transcripts
-##We used DEseq to normalize data.
+*We used DEseq to normalize data.
-##Data can be normalized using a total read count (TC) normalization.
+*Data can be normalized using a total read count (TC) normalization.

← Older revision		Revision as of 17:11, 13 February 2016
Line 1:		Line 1:
	== Classwork ==		== Classwork ==
		+
		+	'''Today in class, we shared group findings from [[January 28, 2016]]:'''
		+	#Blast the overrepresented sequences
		+	*Blast groups found mostly mitochondrial or ribosomal genes.
		+	*Intestine blast group found an amino transferase gene that may be of interest later.
		+	*Liver blast group found an anti-hemorage gene that may be of interest later.
		+
		+
		+	#Attempt to access the list of genes (SRP-0151827) mentioned in the Andrew et al. (2015) study
		+	*We can blast our sequences against the Andrew et al. (2015) library.
		+	*We have the potential to download the entire library with instructions on the website, but do not understand how to use the software/programs required to do so.
		+	*We found a toolkit that allows us to download one sequence at a time.
		+	*We can blast within a run.
		+
		+
		+	#Add numbers to label proteins of "unknown function" in our reads
		+	*Dylan and Dustin made a file that removed duplicate names from our runs.
		+	*Dr. Campbell and Dr. Heyer used their file and got gene mapping results!
		+
		+
		+	#Normalize relative abundance of transcripts
		+	*We used DEseq to normalize data.
		+	*Data can be normalized using a total read count (TC) normalization.

← Older revision	Revision as of 17:01, 13 February 2016
Line 1:	Line 1:
	+	== Classwork ==