January 21, 2016

Article Discussion

"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:

• 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

Ashlyn's Main Page

References

• Castoe, Todd A., et al. “The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.” Pnas.org. (2013)

Castoe et al. (2013)

Supplementary Material