score_min L,0,-1.2 data to test parameters with

[yaaminiv]

I tried using subset sequences from a previous bismark run (see Jupyter notebook and lab notebook) to test differences in 1x, 3x, and 5x coverage in methylkit (see lab notebook). These subset sequences did not have enough data.

I have three options:

1. Find other deduplicated, sorted, and indexed C. virginica full sample data that used -score_min L,0,-1.2 (maybe from @sr320's runs...?) to test coverage with
2. Finish this bismark run on hummingbird and use that output. The files are currently on gannet
3. Wait for my data to eventually come from Mox

I'm leaning towards option 2. Any objections/things I'm not considering?

[sr320]

Subsettting will not provide enough data to get loci for methylkit - I would pursue 1-3 as comparison of outcome will be nice comparison. thanks Steven Steven B. Roberts Kenneth K. Chew Endowed Professor School of Aquatic and Fishery Sciences University of Washington, Seattle WA sr320@uw.edu - 206.866.5141 robertslab.info - @sr320

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On Oct 12, 2018, 4:22 PM -0700, Yaamini Venkataraman ***@***.***>, wrote: I tried using subset sequences from a previous bismark run (see Jupyter notebook and lab notebook) to test differences in 1x, 3x, and 5x coverage in methylkit (see lab notebook). These subset sequences did not have enough data. I have three options: 1. Find other reduplicated, sorted, and indexed C. virginica full sample data (maybe from @sr320's runs) to test coverage with 2. Finish this bismark run on hummingbird. The files are on gannet 3. Wait for my data to eventually come from Mox — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[yaaminiv]

@sr320 Where can I find data from this notebook?

[sr320]

Can be found @ http://gannet.fish.washington.edu/seashell/bu-serine-wd/18-04-29/

…

On Oct 14, 2018, 2:02 PM -0700, Yaamini Venkataraman ***@***.***>, wrote: @sr320 Where can I find data from this notebook? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.