[IGBF-4077] VENN diagram of overlapping genes from De novo - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
3
Epic Link:
Support NSF pollen grant
Sprint:
Spring 1

Description

GOAL: Since we have BLAT mapped most of our de novo genes to SL5, we can produce a large VENN diagram (or UpsetR plot) of how much overlap there is for each time point/temp condition.

Exploit the SolyId imbedded in the fasta header (Brandon created these after the BLAT step).
For an experiment group X4 varieties, we just tally up how often we see a gene.

This gets repeated for each time point. This is about the only way we can get back to comparing across varieties.

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gene_comparison_table.tsv
1.08 MB
29/Jan/25 3:22 PM

Activity

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Robert Reid created issue - 28/Jan/25 1:32 PM

Robert Reid made changes - 28/Jan/25 1:32 PM

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

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Robert Reid added a comment - 29/Jan/25 9:52 AM

Extra IDEA:
Extract from BLAT results!!!!!

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Robert Reid added a comment - 29/Jan/25 9:52 AM Extra IDEA: Extract from BLAT results!!!!!

Brandon Bendickson made changes - 29/Jan/25 9:54 AM

Assignee

Robert Reid [ robertreid ]

Brandon Bendickson [ bbendick ]

Brandon Bendickson made changes - 29/Jan/25 9:54 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Brandon Bendickson made changes - 29/Jan/25 3:22 PM

Attachment

gene_comparison_table.tsv [ 18619 ]

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Brandon Bendickson added a comment - 29/Jan/25 3:23 PM

Made chart to identify matches between blat and other varieties, going to work on making an upset plot in R. gene_comparison_table.tsv

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Brandon Bendickson added a comment - 29/Jan/25 3:23 PM Made chart to identify matches between blat and other varieties, going to work on making an upset plot in R. gene_comparison_table.tsv

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Robert Reid added a comment - 31/Jan/25 10:08 AM

BLAT filtering.
It would be neat to see if we are more conservative with our BLAT score criteria, how that affects the UpsetR plots.

My theory is that as we get more stringent with the score cut off criteria, we might see a cool pattern. I bet Heinz will show more genes as the others will decrease. It would be cool to see a cutoff where the other varieties group together.

More plots, each time changing the score cutoff criteria.

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Robert Reid added a comment - 31/Jan/25 10:08 AM BLAT filtering. It would be neat to see if we are more conservative with our BLAT score criteria, how that affects the UpsetR plots. My theory is that as we get more stringent with the score cut off criteria, we might see a cool pattern. I bet Heinz will show more genes as the others will decrease. It would be cool to see a cutoff where the other varieties group together. More plots, each time changing the score cutoff criteria. R

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Robert Reid added a comment - 31/Jan/25 10:09 AM

Next phase, we do UpsetR plots at each time point. I don't think we can use BLAT table anymore in this case.
That will be a new ticket.

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Robert Reid added a comment - 31/Jan/25 10:09 AM Next phase, we do UpsetR plots at each time point. I don't think we can use BLAT table anymore in this case. That will be a new ticket.

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Robert Reid added a comment - 07/Feb/25 10:13 AM

The UpsetR plots that have been generated are good enough to go into the presentation.

Pop those in and then we can close this ticket.

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Robert Reid added a comment - 07/Feb/25 10:13 AM The UpsetR plots that have been generated are good enough to go into the presentation. Pop those in and then we can close this ticket.