2/6/18

FastQC: Quality control to see how the run went, and the quality of our data. Uses quality read information to give us an image/graph

Trimmomatic: Takes of lower quality reads as well as removed adaptor sequence. Uses quality read information to chop of low quality data.

-Four lines -@identified -Bases -+ other information : has quality read information

r1- forward r2-reverse

Tophat: Aligns sequences to mamilian genome. A challenge arises because mapping needs to take place with gaps because of introns that are removed in mature RNA. Similar more updated program called HISAT2, thats faster but does the same thing as Tophat. Yeilds a BAM/SAM file. Tells where sequence aligns to gene.

Cufflinks: FPKM values Must input annotation file( gff/gtf) and tophat file. Gives number of reads. Used HTseq (a newer version).

What Dr. Campbell & Dr. TS did:

The mapping to genome (HISAT), HISeq, then DEseq2 ( where we get to do the difference between samples we choose).