[IGBF-3246] Generate list of EBSeq-HMM clusters for varieties and conditions - JIRA UNCC

Ann Loraine created issue - 01/Feb/23 10:23 AM

Ann Loraine made changes - 01/Feb/23 10:23 AM

Field	Original Value	New Value
Epic Link		IGBF-2993 [ 21429 ]

Ann Loraine made changes - 01/Feb/23 10:23 AM

Link

This issue relates to ~~IGBF-3242~~ [ ~~IGBF-3242~~ ]

Ann Loraine made changes - 01/Feb/23 10:23 AM

Link

This issue relates to ~~IGBF-3244~~ [ ~~IGBF-3244~~ ]

Molly Davis made changes - 02/Feb/23 9:46 AM

Description

Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

* Create a new git repository for clustering code within hotpollen for the code
* Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system
* Run EB-Seq on the merged file
* Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
* Share with collaborators: results files and markdown report

Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

* Create a new git repository for clustering code within hotpollen for the code
*{color:#14892c} Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system {color}
* {color:#14892c}Run EB-Seq on the merged file{color}
* Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
* Share with collaborators: results files and markdown report

Molly Davis made changes - 02/Feb/23 9:47 AM

Description

Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

* Create a new git repository for clustering code within hotpollen for the code
*{color:#14892c} Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system {color}
* {color:#14892c}Run EB-Seq on the merged file{color}
* Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
* Share with collaborators: results files and markdown report

Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

* Create a new git repository for clustering code within hotpollen for the code
* {color:#14892c} Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system {color}
* {color:#14892c}Run EB-Seq on the merged file{color}
* Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
* Share with collaborators: results files and markdown report

Molly Davis made changes - 02/Feb/23 10:06 AM

Attachment

mark-timeseries-SL5-salmoncounts.txt [ 17669 ]

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Molly Davis added a comment - 02/Feb/23 10:07 AM - edited

Update:

Dr. Reid created a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system.
File: mark-timeseries-SL5-salmoncounts.txt
I ran EB-Seq on the merged file and produced cluster path txt files.
I am still trying to figure our how to create human readable files. I am having difficulty making it a spreadsheet because there would be a different number of rows or columns to each label.
Currently also trying to make Venn diagrams to compare cluster files.

Next Step: Make directory and share with collaborators.

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Molly Davis added a comment - 02/Feb/23 10:07 AM - edited Update: Dr. Reid created a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system. File: mark-timeseries-SL5-salmoncounts.txt I ran EB-Seq on the merged file and produced cluster path txt files. I am still trying to figure our how to create human readable files. I am having difficulty making it a spreadsheet because there would be a different number of rows or columns to each label. Currently also trying to make Venn diagrams to compare cluster files. Next Step: Make directory and share with collaborators.

Molly Davis made changes - 02/Feb/23 10:07 AM

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Molly Davis [ molly ]

Molly Davis made changes - 02/Feb/23 11:05 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Ann Loraine added a comment - 02/Feb/23 11:31 AM - edited

Result from today's discussion:

1) Run the clustering algorithm on the following sample groups:

Heinz stress, MP, 30 min, 60 min, 120 min
Heinz control, MP, 30 min, 60 min, 120 min
Tamaulipas stress, MP, 30 min, 60 min, 120 min
Tamaulipas control, MP, 30 min, 60 min, 120 min
Nagcarlang stress, MP, 30 min, 60 min, 120 min
Nagcarlang control, MP, 30 min, 60 min, 120 min

This will create some EBSeq-HMM objects corresponding to clusters, where each cluster has a name like "UP-UP-UP".

2) Next, write out them into one tab-separated file with the following columns:

cluster name (e.g., UP-UP-UP)
SL5 gene name
genotype (e.g., Heinz, Nagcarlang or Tamaulipas)
temperature (e.g., C.28, S.34)

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Ann Loraine added a comment - 02/Feb/23 11:31 AM - edited Result from today's discussion: 1) Run the clustering algorithm on the following sample groups: Heinz stress, MP, 30 min, 60 min, 120 min Heinz control, MP, 30 min, 60 min, 120 min Tamaulipas stress, MP, 30 min, 60 min, 120 min Tamaulipas control, MP, 30 min, 60 min, 120 min Nagcarlang stress, MP, 30 min, 60 min, 120 min Nagcarlang control, MP, 30 min, 60 min, 120 min This will create some EBSeq-HMM objects corresponding to clusters, where each cluster has a name like "UP-UP-UP". 2) Next, write out them into one tab-separated file with the following columns: cluster name (e.g., UP-UP-UP) SL5 gene name genotype (e.g., Heinz, Nagcarlang or Tamaulipas) temperature (e.g., C.28, S.34)

Molly Davis made changes - 06/Feb/23 4:11 PM

Attachment

EBSeq_tomato.Rmd [ 17670 ]

Molly Davis made changes - 06/Feb/23 4:12 PM

Attachment

all_data_clusters.csv [ 17671 ]

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Molly Davis added a comment - 06/Feb/23 4:12 PM

Made commit to bitbucket:

https://bitbucket.org/hotpollen/time-series/commits/cd23c7c2c4688e470925d063a11c0b225800e07c

Includes R markdown, count file, and a final dataframe as a csv file.

EBSeq_tomato.Rmd
mark-timeseries-SL5-salmoncounts.txt
all_data_clusters.csv

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Molly Davis added a comment - 06/Feb/23 4:12 PM Made commit to bitbucket: https://bitbucket.org/hotpollen/time-series/commits/cd23c7c2c4688e470925d063a11c0b225800e07c Includes R markdown, count file, and a final dataframe as a csv file. EBSeq_tomato.Rmd mark-timeseries-SL5-salmoncounts.txt all_data_clusters.csv

Molly Davis made changes - 06/Feb/23 4:16 PM

Description

Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

* Create a new git repository for clustering code within hotpollen for the code
* {color:#14892c} Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system {color}
* {color:#14892c}Run EB-Seq on the merged file{color}
* Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
* Share with collaborators: results files and markdown report

Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

* Create a new git repository for clustering code within hotpollen for the code
* Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system
* Run EB-Seq on the merged file
* Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
* Share with collaborators: results files and markdown report

Molly Davis made changes - 06/Feb/23 4:16 PM

Assignee

Molly Davis [ molly ]

Molly Davis made changes - 06/Feb/23 4:16 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

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Molly Davis added a comment - 08/Feb/23 10:24 AM - edited

Update:

[~RobertReid] reviewed the files.

Need to do:

Change print commands to just include head() of tables.
Add files to drive for tomato group
Drive location: https://drive.google.com/drive/folders/1_I6PLSoBg4H3Y1MzY2qhxjk-FBmM4cmQ?usp=share_link
Update bitbucket with new changes to Rmd file with commit.

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Molly Davis added a comment - 08/Feb/23 10:24 AM - edited Update: [~RobertReid] reviewed the files. Need to do: Change print commands to just include head() of tables. Add files to drive for tomato group Drive location: https://drive.google.com/drive/folders/1_I6PLSoBg4H3Y1MzY2qhxjk-FBmM4cmQ?usp=share_link Update bitbucket with new changes to Rmd file with commit.

Molly Davis made changes - 10/Feb/23 2:54 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Molly Davis made changes - 10/Feb/23 2:54 PM

Status

First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

Molly Davis made changes - 10/Feb/23 2:54 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Molly Davis made changes - 10/Feb/23 2:55 PM

Assignee

Molly Davis [ molly ]