Difference between revisions of "January 21, 2016"
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== Article Discussion == | == 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" === |
| + | |||
| + | *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 | ||
| + | *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 == | == Classwork == | ||
| + | === 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. | ||
| + | *All reads are 76bp. | ||
| + | *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:''''' | ||
| + | '''''*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.''''' | ||
| + | |||
| + | ''INCLUDE SCREENSHOTS OF DATA WHEN YOU FIGURE OUT HOW TO UPLOAD PICTURES'' | ||
[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] | ||
| + | |||
| + | |||
Revision as of 14:48, 13 February 2016
Contents
Article Discussion
"The Burmese Pythod Genome Reveals the Molecular Basis for Extreme Adaptation in Snakes"
- 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
- 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
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.
- All reads are 76bp.
- 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: *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.
INCLUDE SCREENSHOTS OF DATA WHEN YOU FIGURE OUT HOW TO UPLOAD PICTURES
References
- Castoe, Todd A., et al. “The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.” Pnas.org. (2013)
