Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Fall 1, Fall 2
Description
GOAL: Now that we have a merged NEXTFLOW salmon counts table derived from the de novo rna-SPades assembly, we combine want to compare the original NETFLOW results (reference based) to the newly merged de novo table.
Step 1 is to make an EVEN bigger table. Each row is a gene.
To start I suggest the table be for only 1 variety ( all NAG, e.g.,).
We create this 1 table. And then apply Deseq2 and a PCA to see what results we get. Do they various time points align perfectly when comparing the de novo to the reference based?
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Assignee | Ann Loraine [ aloraine ] | Robert Reid [ robertreid ] |
| Assignee | Robert Reid [ robertreid ] | Brandon Bendickson [ bbendick ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Brandon Bendickson [ bbendick ] | Robert Reid [ robertreid ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Sprint | Fall 1 [ 202 ] | Fall 1, Fall 2 [ 202, 203 ] |
| Rank | Ranked higher |
| Assignee | Robert Reid [ robertreid ] | Brandon Bendickson [ bbendick ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Successfully merged all de novo runs with previous runs.
Results are in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/result_processing/combine_old_and_new
Checked the files to make sure we didn't lose anything
-bash-4.4$ wc -l Heinz_merged.tsv
24832 Heinz_merged.tsv
-bash-4.4$ wc -l Malintka_merged.tsv
24841 Malintka_merged.tsv
-bash-4.4$ wc -l Nagcarlang_merged.tsv
24697 Nagcarlang_merged.tsv
-bash-4.4$ wc -l Tamaulipas_merged.tsv
25357 Tamaulipas_merged.tsv
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Brandon Bendickson [ bbendick ] | Robert Reid [ robertreid ] |
I checked out merge.py in the above folder.
It is a clean script using pandas!! Great work.
I think this naming conventin works really well:
M.25C.0hr.S.2.R1.fastq.gz.denovo
Malintka.R3.0hr.25C.ref ......
I think this ticket is ready for closing!
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
I found an issue where I lost sequences when modifying my de novo counts files. I remade the counts files and got the right number of sequences. I merged the de novo runs with the old NEXTFLOW runs. From what I can tell, the de novo runs map closely to the old runs.
My merged files are located in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/result_processing/combine_old_and_new
I would disregard Nag for now. I may have to rerun RNA spades for Nag as per ticket #3901.
Moving this to first level review.