Genomics in the Pinsky Lab

From fish to SNPs, many steps are involved in obtaining and processing our data.

• Sample collection can be found in the field repository.

• Sample processing through sequence submission can be found in the laboratory repository.

• Sequence processing through identity analysis (mark recapture) can be found here in the genomics repository.

  1. Receive and prepare sequences for SNP calling
  2. Call SNPs
  3. Plot the raw SNPs to visualize the data
  4. Filter SNPs
  5. Remove regenotyped individuals
  6. Identify recaptured individuals
  7. Update recaptured RData file

Open this Rproject on the RStudio Server on amphiprion to use for steps 1-4 (i-iv).
Our reference.fasta file was assembled by Jon Puritz using dDocent and 300 individuals from our APCL sample set.

Navigation

Protocols

Step by step guides to processing sequencing data. Make a copy of these files and update that copy with the specifics you encountered during your analysis to serve as a lab notebook. The protocols listed in the steps above. If vieiwng on github, the .md files are the easiest way to view these files. If you want to run the scripts, open the .Rmd files through RStudio or render them with regular R by typing into the R command line:

rmarkdown::render("file_name.Rmd")

R

Old scripts that are no longer used but may be helpful for problem solving.

data

Data files required to run the scripts.

filtering

Scripts for filtering vcf files.

lab-notebooks

Records of how sample runs were processed. A copy of the protocol step was saved into this folder and renamed to represent the samples that were being worked on. These are best viewed as html files.

manuals

Manufacturer manuals and guides.

plots

all-mismatch-prop.png - graph of the mismatch proportions of all comparisons of identity analysis.

plot-clownfish-at-size-change-M-to-F.md

• graphic output version of the code to produce plots.

[plot-clownfish-at-size-change-M-to-F.Rmd](plots/plot-clownfish-at-size-change-from-M-t