Pipeline modificaitons

Cluster 1:

Cluster composition post all filters:

1. CLUSTER1:

Comparison of results for the following data after adding an additional filter (Filter2b) for removing outlier samples identified by DAPC and rerunning the full epiRAD pipeline.

Number of individuals left after this additional filter is 33.

Comparison of ddARD data analysis results for sample subgroups

Pop Gen Analysis

dDocent was used for QC, assembly, mapping and SNP calls on raw ddRAD data. dDocent SNP filtering pipeline plus rad haplotyper was used for filtering SNPs. Input file: SNP.DP3g95p5maf001.HWE.filtered.vcf.gz

Comparison of results for the following data after removing outlier samples

1. Filter4: Data obtained post BLAST filter, low read filter and low coverage filter
2. Filter 5a: Data obtained post filter4 AND removing problematic loci identified by rad_haplotyper
3. Filter 5b: Data obtained post filter4 AND keeping only those loci that remain after full SNP filtering pipeline

Comparison of results for

1. Filter4: Data obtained post BLAST filter, low read filter and low coverage filter
2. Filter 5a: Data obtained post filter4 AND removing problematic loci identified by rad_haplotyper
3. Filter 5b: Data obtained post filter4 AND keeping only those loci that remain after full SNP filtering pipeline

Step1: 50% of individuals, a minimum quality score of 30, and a minor allele count of 3

Step2: Minimum mean depth Testing at 2 values

With the full dataset testing 2 values of minDP

SNP filtering

This filtering was performed on full data set per the [ SNP filtering tutorial ] (http://www.ddocent.com/filtering/) in dDocent. The filtration is housed in /home/tejashree/Moorea/ddocent/final/snp_filtering/.

Methylation data

Reference fasta

Running a test assembly on a subset of data

SNP filtering

Running a test assembly on a subset of data

Getting the data

• Data was copied from Hollie’s disk to KITT /RAID_STORAGE2/Shared_Data/20190819_RAD_EPIRAD/30-233732769/
• I copied it from here to my dir tejashree/Moorea/raw_data/

Barcode files

1. Barcode files were made from the csv file on google drive Moorea_2018_Sampling Adapter/Index Map

Mo’orea Project Background

This project is a part of LTER Network. Mo’orea is a part of French Polynesia. The coral reef in the northern region of the island was adversely affected by two natural events. However, over time the reef came back to a healthy state.
In order to understand re-colonization of these regions this project has multiple layers.

1. Studying re colonization patterns in this region has long term and broad applications associated with climate change.
2. Study sites vary in type of water dynamics, depth and temperature conditions. As such understanding the colonization patterns in light of these environmental variables has applications associated with rising water temperatures and climate change.

   Goal

3. Use ddRAD to understand population dynamics across sampling sites
4. Use epiRAD along with ddRAD to understand epigenetic patterns with respect to habitat variables

   Study site

   

   Sampling

   8 sites sampled with up to 15 samples of Porites (lobata/lutea) and Pocillopora (meandrina/verrucosa) per site.

   Sequencing

   ddRAD and epiRAD with a methylation sensitive restriction enzyme used in epiRAD (Schield et al. 2016).