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" (2013) === |
*Researchers clustered genes with similar trends in differential gene expression together. | *Researchers clustered genes with similar trends in differential gene expression together. | ||
*STEM is a source of gene identifiers and clusters. | *STEM is a source of gene identifiers and clusters. | ||
| − | *Volcano plots showed significant difference for no change in gene expression levels. | + | *Volcano plots showed significant difference for no change in gene expression levels. |
| − | + | === Questions to Consider: === | |
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| − | |||
| − | === Questions to Consider === | ||
*What are the names of the genes the researchers clustered? | *What are the names of the genes the researchers clustered? | ||
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*What started the cascade? | *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? | + | *If a few genes don't change, is that biologically significant? |
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| − | |||
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== Classwork == | == 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. | *A quality score above 40 is good. | ||
*Sequence codes match the reagents provided in class document. | *Sequence codes match the reagents provided in class document. | ||
| Line 32: | Line 26: | ||
*Overall, our data is of good quality. | *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. |
Latest revision as of 17:00, 13 February 2016
Contents
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
References
- Castoe, Todd A., et al. “The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.” Pnas.org. (2013)
