January 21, 2016 - Revision history

Asgruber: /* Analyze FastQC data analysis results downloaded from class on January 19, 2016 */

2016-02-13T17:00:49Z

‎Analyze FastQC data analysis results downloaded from class on January 19, 2016

2016-02-13T14:54:54Z

‎Questions to Consider

2016-02-13T14:53:59Z

‎"The Burmese Pythod Genome Reveals the Molecular Basis for Extreme Adaptation in Snakes"

2016-02-13T14:52:32Z

2016-02-13T14:51:48Z

2016-02-13T14:48:17Z

2016-02-12T19:28:23Z

‎Classwork:

2016-02-12T19:28:13Z

‎Article Discussions:

2016-02-12T19:25:40Z

@@ Line 17: / Line 17: @@
 == Classwork ==
-=== Analyze FastQC data analysis results downloaded from class on January 19, 2016 ===
+=== Analyze FastQC data analysis results downloaded from class on [[January 19, 2016]] ===
 *A quality score above 40 is good.
 *Sequence codes match the reagents provided in class document.

@@ Line 7: / Line 7: @@
 *Volcano plots showed significant difference for no change in gene expression levels.
-=== Questions to Consider ===
+=== Questions to Consider: ===
 *What are the names of the genes the researchers clustered?
@@ Line 13: / Line 13: @@
 *What started the cascade?
 **If known '''''transcription factors''''' activate genes in the cascade, maybe we can find them early on.
 *If a few genes don't change, is that biologically significant?
 == Classwork ==

@@ Line 1: / Line 1: @@
 == Article Discussion ==
-=== "The Burmese Pythod Genome Reveals the Molecular Basis for Extreme Adaptation in Snakes" ===
+=== "The Burmese Pythod Genome Reveals the Molecular Basis for Extreme Adaptation in Snakes" (2013) ===
 *Researchers clustered genes with similar trends in differential gene expression together.
 *STEM is a source of gene identifiers and clusters.
 *Volcano plots showed significant difference for no change in gene expression levels.
 === Questions to Consider ===

@@ Line 6: / Line 6: @@
 *STEM is a source of gene identifiers and clusters.
 *Volcano plots showed significant difference for no change in gene expression levels.
@@ Line 17: / Line 16: @@
 **If known '''''transcription factors''''' activate genes in the cascade, maybe we can find them early on.
 *If a few genes don't change, is that biologically significant?
@@ Line 32: / Line 30: @@
 *Overall, our data is of good quality.
 '''''Moving forward, we need to:
 *Trim off the first 4 bases.
 *Discard reads with a score less than 15.
 *Name all the reads.
 *Sort all the reads.
-*Exhaust publicly avaible data sets.'''''
+*Exhaust publicly avaible data sets.

@@ Line 5: / Line 5: @@
 *Researchers clustered genes with similar trends in differential gene expression together.
 *STEM is a source of gene identifiers and clusters.
 *Volcano plots showed significant difference for no change in gene expression levels.
 === Questions to Consider ===
 *What are the names of the genes the researchers clustered?
-***Investigate ncbi gene bank
+**Investigate ncbi gene bank
 *What started the cascade?
-***If known '''''transcription factors''''' activate genes in the cascade, maybe we can find them early on.
+**If known '''''transcription factors''''' activate genes in the cascade, maybe we can find them early on.
 *If a few genes don't change, is that biologically significant?
@@ Line 27: / Line 29: @@
 *Very few "N's." A "N" indicates that RNAseq was unable to pick a base.
 *Intestine has smooth GC curve line.
 *The class was unable to determine what exactly "Sequence Duplication Levels" showed us.
-'''''Overall, our data is of good quality. Moving forward, we need to:'''''
+'''''Moving forward, we need to:
-'''''*Trim off the first 4 bases.'''''
+*Trim off the first 4 bases.
-'''''*Discard reads with a score less than 15.'''''
+*Discard reads with a score less than 15.
-'''''*Name all the reads.'''''
+*Name all the reads.
-'''''*Sort all the reads.'''''
+*Sort all the reads.
-'''''*Exhaust publicly avaible data sets.'''''
+*Exhaust publicly avaible data sets.'''''
 ''INCLUDE SCREENSHOTS OF DATA WHEN YOU FIGURE OUT HOW TO UPLOAD PICTURES''

← Older revision		Revision as of 19:28, 12 February 2016
Line 3:		Line 3:
	=== "The Burmese Pythod Genome Reveals the Molecular Basis for Extreme Adaptation in Snakes" ===		=== "The Burmese Pythod Genome Reveals the Molecular Basis for Extreme Adaptation in Snakes" ===

−	== Classwork: ==	+	== Classwork ==

← Older revision		Revision as of 19:28, 12 February 2016
Line 1:		Line 1:
−	== Article ~~Discussions:~~ ==	+	== Article Discussion ==
−
−	~~=== "The Burmese Pythod Genome Reveals the Molecular Basis for Extreme Adaptation in Snakes" ===~~

		+	=== "The Burmese Pythod Genome Reveals the Molecular Basis for Extreme Adaptation in Snakes" ===

	== Classwork: ==		== Classwork: ==

← Older revision	Revision as of 19:25, 12 February 2016
Line 7:	Line 7:


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