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Develop taxa comparison of methylation via Bismark #589

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sr320 opened this issue Feb 19, 2019 · 6 comments

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commented Feb 19, 2019

Concatenate all BS reads for each species (Cv, Cg, Pg, Ol) then randomly sample set number of reads.
Align to the respective genome using Bismark.

for talk next week. Thinking some number of reads that could "easily" map leveraging coenv node etc. Maybe start conservatively.

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commented Feb 25, 2019

Here's mapping efficiencies of all except geoduck (this will complete late tonight, I think - will post here when finished).

Notebook posts are in the works, but the results below are untrimmed, R1 reads only, for each species (paired-end Bismark analysis didn't yield any results for mapping efficincies - like that part of the report is just empty).


C.gigas

Reads Subset Mapping Efficiency (%)
100000 55.0
500000 55.1
1000000 55.1
2000000 55.0
5000000 54.9
10000000 54.2

C.virginica

Reads Subset Mapping Efficiency (%)
100000 18.5
500000 18.6
1000000 19.2
2000000 19.5
5000000 18.6
10000000 16.1

O.lurida

Reads Subset Mapping Efficiency (%)
100000 54.2
500000 54.4
1000000 54.5
2000000 54,4
5000000 54.3
10000000 53.8
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commented Feb 25, 2019

P.generosa

Genome Reads Subset Mapping Efficiency (%)
v070 100000 56.3
v070 500000 56.1
v070 1000000 56.1
v070 2000000 56.2
v070 5000000 56.2
v070 10000000 56.2
v071 100000 54.1
v071 500000 53.8
v071 1000000 53.9
v071 2000000 53.9
v071 5000000 54.0
v071 10000000 53.9
v073 100000 49.8
v073 500000 49.7
v073 1000000 49.7
v073 2000000 49.7
v073 5000000 49.8
v073 10000000 49.7

EDITED: Added last two lines of table that were originally omitted.

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commented Feb 25, 2019

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commented Feb 25, 2019

Would a bedgraph suffice?

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commented Feb 25, 2019

@sr320 sr320 closed this Mar 4, 2019

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