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:2
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Epic Link:
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Sprint:Fall 2, Fall 3, Fall 4, Fall 5, Fall 6
Description
Purpose: To submit the de novo assembled RNA-Seq contigs to NCBI's TSA archive.
Since our raw reads already exist as a SRA, this should be straightforward. I just need to align reads to assemblies and the upload assemblies.
Attachments
Issue Links
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- Closed
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Activity
I submitted this again.
I am closing the ticket!
We will generate a new ticket if needed.
The 2 filtering steps are:
FCS_adaptor
FCS_GX
Brandon successfully ran the filtering steps and the results are here:
/projects/tomato_genome/fnb/dataprocessing/TSA-transcriptomeShotgunAssembly/kelsieData/FCS_tools/FCS_GX/tom_runs/fin_results
I am pulling them down locally and then uploading to the TSA.
Bringing this back one more time!!
Will submit the sequences once they get filtered using NCBI filter tool (Ticket IGB-3966)
We get filtered reads via NCBI tool.
Rob reloads to TSA ONE MORE time.
Accidentally put this comment on ticket 3944: Modified script, results found in Kelsie data. I wrote function that looked at the last 12 characters, and if there was an N in those 12 it removed the all 12. Should be ready for resubmission. May it please the TSA gods.
TSA submission: SUB14767088
1st step is the Fasta asembly uploads to FTP. After tthat, they ask for the metadata. Backwards to SRA and GEO.
Noter from Brandon where the final contigs are:
Removed duplicates and wrote them to their own file (Variety_dupes.fa). The new files are located in /projects/tomato_genome/fnb/dataprocessing/TSA-transcriptomeShotgunAssembly/kelsieData/FCS_tools/FCS_GX/tom_runs/fin_results
They follow this pattern (Variety_contaminant3_removed.fa), We should be ready for another submission. Python script is fix_contam3_v2.py and is in same directory