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pinskylab / genomics

Wrangling of genomic data and identity analysis
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Number of fish_indiv changed #36

Closed mstuart1 closed 5 years ago

mstuart1 commented 5 years ago

the number of individually identified fish (so number of distinct fish_indiv values) went down by about 360 fish since my previous run - it was 3413 individual fish in my last draft and is now at 3053. The number of individual PIT-tags (1929) hasn’t changed but the number of gen_ids is down by a similar number (from 2772 to 2406). @Michelle Stuart, did anything change with gen_ids in the last few months that would have caused the overall number to drop? If anything, I would have thought the recent updates to fish_indiv (https://pinskylab.slack.com/archives/CKN1KGGBW/p1567801201002600) would have increased the number of individually-identified fish slightly.

mstuart1 commented 5 years ago

2893 fish were genotyped as of SEQ31 (our most recent seq run) 2824 fish do not have "known issues" 2772 fish remain after regenotypes are removed + 1047 fish obs that have been tagged but not genotyped = 3819 (05_remove-regenos.Rmd)

now the fish-obs.Rdata (rds, csv) file has 3819 rows.

In 06_identity-protocol.Rmd, the gen_ids change to match recapture events, but the number of columns in fish-obs doesn't change and there is no fish_indiv column yet.

Recaptures are removed from the gene pop, which goes down to 2406 rows (fish).

in 07_recaptured-fish.Rmd, fish_indiv column is created and assigned to fish. There are still 3819 rows in the file.

mstuart1 commented 5 years ago

unique(fish_indiv) = 3053 unique(tag_id) = 1930 unique(gen_id) = 2407