Difference between revisions of "February 2, 2016"
From GcatWiki
(→Classwork) |
(→Classwork) |
||
| Line 30: | Line 30: | ||
| + | [http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Ashlyn Ashlyn's Main Page] | ||
| − | [http:// | + | |
| + | |||
| + | <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)] | ||
Revision as of 17:15, 13 February 2016
Classwork
Today in class, we shared group findings from January 28, 2016:
1. 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.
2. 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.
3. 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!
4.Normalize relative abundance of transcripts
- We used DEseq to normalize data.
- Data can be normalized using a total read count (TC) normalization.
References"
- 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.
