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pinskylab / genomics

Wrangling of genomic data and identity analysis
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fish in 2012-2015 sequencing data without gen_ids #6

Closed katcatalano closed 5 years ago

katcatalano commented 5 years ago

The R data file in this file is a table of sample_ids that are in the sequencing data, but don't attach to a gen_id. Let me know if you want it in a different format.

mstuart1 commented 5 years ago

I can't open that because it is private. When I go to your GitHub page it says you have 0 repos. Can you upload the file to this genomics repo?

katcatalano commented 5 years ago

Sorry about that, I uploaded the .rds to pinskylab/genomics/data!

mstuart1 commented 5 years ago

I'm about to begin looking into these but as I started to make notes, I remembered that you had looser criteria for your samples than I did, so samples that were filtered out of my data set were included in yours and that might be why these samples don't have gen_ids.

When we discussed creating the gen_id column, Malin said to use the stricter criteria to consider a sample successfully sequenced.

This is also why you have a couple thousand loci in your past analysis compared to the ~1000 (or 860?) that I filtered out at that time.

katcatalano commented 5 years ago

Cool, that makes sense. Thanks!

mstuart1 commented 5 years ago

There were 2 samples in your list that looked like they should have a gen_id, so I added the gen_id to those samples. Redownload data from the database for the freshest version.

Cheers.