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homework_6_ancestry [2015/11/15 11:31] scott |
homework_6_ancestry [2015/11/16 10:18] scott |
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### ONLY EXPLAIN COMMANDS WHERE I SPECIFICALLY REQUEST IT! YOU DO NOT | ### ONLY EXPLAIN COMMANDS WHERE I SPECIFICALLY REQUEST IT! YOU DO NOT | ||
- | ### HAVE TO EXPLAIN EVERY COMMAND! | + | ### HAVE TO EXPLAIN EVERY COMMAND! |
+ | ### in the end a PCA plot containing yourself compared to all 1000 Genomes | ||
+ | ### samples. | ||
# For many questions you'll want to run analyses by chromosome. To do | # For many questions you'll want to run analyses by chromosome. To do | ||
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module load apigenome_0.0.2 | module load apigenome_0.0.2 | ||
module load plink_latest | module load plink_latest | ||
+ | module load tabix_0.2.6 | ||
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### Retain in the 1000 Genomes VCF only your SNPs that are also fairly common | ### Retain in the 1000 Genomes VCF only your SNPs that are also fairly common | ||
- | ### | + | ### because we're going to conduct PCA on these SNPs and only want common ones. |
- | ###------ QUESTION 3: WHY WOULD WE REMOVE | + | ### |
+ | ###------ QUESTION 3: WHY WOULD WE RETAIN ONLY COMMON SNPS, OTHER THAN IT | ||
### | ### | ||
for i in {1..22}; do | for i in {1..22}; do | ||
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### ' | ### ' | ||
- | kg_sf <- read.table('/ | + | kg_sf <- read.table('/ |
sample_ids <- unique(data.frame(IID=kg_sf$SAMPLE_NAME, | sample_ids <- unique(data.frame(IID=kg_sf$SAMPLE_NAME, |