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
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
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!
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.