generate a conical coverage track for each coral methylome using 9 samples at 5x coverage

[sr320]

Mcap available @ https://github.com/hputnam/Meth_Compare/blob/master/scripts/10-Mcap-Canonical-Coverage-Track.ipynb

[sr320]

Pact available @ https://github.com/hputnam/Meth_Compare/blob/master/scripts/11-Pact-Canonical-Coverage-Track.ipynb

[sr320]

really cool comparisons can be made with output as I have methylation level for each sample written out.

Direct link to bedgraphs https://gannet.fish.washington.edu/seashell/bu-github/Meth_Compare/analyses/10-unionbedg/

[hputnam]

@sr320 is it possible to do this for C1 as well?

[sr320]

Running Pact on C1 now... any hints at where Mcap libraries mapped to C1 live?

[hputnam]

There is no mapping for Sym for Mcap. We do not have genomes for their dominant symbionts (C17/C31, D1)

[sr320]

Pact (1-9) on C1 @ https://gannet.fish.washington.edu/seashell/bu-github/Meth_Compare/analyses/10-unionbedg/

nb https://github.com/hputnam/Meth_Compare/blob/master/scripts/12-Pact-C1-Canonical-Coverage-Track.ipynb

[hputnam]

@sr320 I think the C1 got mapped or copied as P acuta instead. The file size is the same and the scaffold name matches the Pacuta genome and not the C1 genome

[hputnam]

something has gone wrong by step 7 in your notebook... scaffolds should look like this

[sr320]

I believe it is now resolved… please do confirm On Apr 1, 2020, 1:59 PM -0700, Hollie Putnam notifications@github.com, wrote:

something has gone wrong by step 7 in your notebook... scaffolds should look like this — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[hputnam]

Yes, the C1 scaffolds are there. Thanks!

[sr320]

Revisiting unionbed... nothing is dependent on this, rather a curiosity to see how much data we have per species..

[sr320]

@shellytrigg you have completed this?

[sr320]

Yes see https://github.com/hputnam/Meth_Compare/issues/43#issuecomment-619280654