search

hputnam / project_juvenile_geoduck_OA

This repository provides data and scripts to analyze the influence of ocean acidification on juvenile geoduck DNA methylation and phenotype.
4 stars 3 forks source link

Day 10 analysis #14

Closed seanb80 closed 7 years ago

seanb80 commented 7 years ago

IGV xml here

RMD for the code here

Raw data here

sr320 commented 7 years ago

Sean - can you work on creating a narrative "lab notebook" entry each day? Similar to those @ http://faculty.washington.edu/sr320/?page_id=246 (Sam's is always a good one to look to)

Can do at genefish.wordpress but I am open to discuss other options such as GitHub (see Hollie's). It should essentially be written for public. Also could imagine Hollie or I having a quick look, and not really having any questions as everything is there. Thanks

On Fri, Jan 27, 2017 at 4:03 PM seanb80 notifications@github.com wrote:

IGV xml here http://owl.fish.washington.edu/scaphapoda/Sean/Day10/results/igv_session.xml

RMD for the code here http://rpubs.com/seanb80/245101

Raw data here http://owl.fish.washington.edu/scaphapoda/Sean/Day10/

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/hputnam/project_juvenile_geoduck_OA/issues/14, or mute the thread https://github.com/notifications/unsubscribe-auth/AEPHt5phCNws0JU_SLDkf91v8LVC8H9vks5rWoW-gaJpZM4LwV6X .

seanb80 commented 7 years ago

I wrote out this on gene fish, is it what you had in mind?

https://genefish.wordpress.com/2017/01/29/dmr-analysis-for-day-10-geoduck-samples/

hputnam commented 7 years ago

@sr320 @seanb80 After looking at the boxplots it seems we have several different patterns by treatment. What do you think about clustering the DML patterns and plotting by samples grouped by treatment similar to "Automatically Partitioning Genes into Expression Clusters" used in Trinity (e.g., https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Differential-Expression)

expression_clusters

I think this could help us condense our box plots and give us patterning to interpret annotations.

seanb80 commented 7 years ago

Count files located at http://owl.fish.washington.edu/scaphapoda/Sean/count_files/

the 3/5/7/10x at the end of each file name signifies the different cutoff levels used.

On Tue, Feb 7, 2017 at 8:47 PM, Hollie Putnam notifications@github.com wrote:

@seanb80 https://github.com/seanb80 could you point me to the location for the Methylation and Total Coverage count files that are going into MACAU?

@sr320 https://github.com/sr320 @seanb80 https://github.com/seanb80 After looking at the boxplots it seems we have several different patterns by treatment. What do you think about clustering the DML patterns and plotting by samples grouped by treatment similar to "Automatically Partitioning Genes into Expression Clusters" used in Trinity (e.g., https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Differential- Expression)

[image: expression_clusters] https://cloud.githubusercontent.com/assets/5198996/22723835/869f8134-ed8f-11e6-9de4-d1b260b9ac8c.jpg

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/hputnam/project_juvenile_geoduck_OA/issues/14#issuecomment-278228346, or mute the thread https://github.com/notifications/unsubscribe-auth/AKIJepWNePWKvuzeH_V2M4pGOe1D8QO0ks5raUjigaJpZM4LwV6X .

hputnam commented 7 years ago

Thanks @seanb80 I will try the clustering analysis.