NHE Jan 21 Notes
From GcatWiki
Reading the HTML fastQC report:
- left side of the widow will tell you whether or not the specific measurement was good
- Good quality scores (40)
- Good sequence quality (>20 mean score) for vast majority of sets
- Can tell the bar codes from the Per base sequence content
Will trim the sequences to remove the barcodes, throw out any reads under 30 bp, and reads with nucleotide scores bellow 15
Intestine has more uniformity in the curves for Mean GC content
- jagged peaks occur more in liver
Nearly 0 uncalled bases (N's) Uniform Lengths
Deduplicated Sequences seem to have the majority
- will run quality control again after remove the bar codes
Don't know what the Overrepresented Sequences are
- might want to blast them ourselves
Adapter Content - makes sure that the primers aren't incorporated. They aren't
We have pretty high quality data
Python Genome Paper
- Transcriptome
- compared to King Cobra
- "redesigned metabolic pathway"
Fig 1 Panel C
- transcriptome array
- light is low transcription
- every array is only 300 genes
- these are the genes that changed the most
- similar behaving genes are blocked together
Panel F
- DNA replication does seem to be unregulated in the intestine, even if most growth is attributed to hypertrophy
Fig 2B
- Mitochondria genes probably nuclear
