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  1. IGB
  2. IGBF-3928

Shotgun assembly submission to the TSA

        Details

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

          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.

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              Task - A task that needs to be done. IGBF-3944 Python script to remove NCBI's contaminants

              • Major - Major loss of function.
              • Closed

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                12 older comments
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                bbendick Brandon Bendickson added a comment -

                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.

                Show
                bbendick Brandon Bendickson added a comment - 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.
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                robofjoy Robert Reid added a comment -

                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.

                Show
                robofjoy Robert Reid added a comment - 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.
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                robofjoy Robert Reid added a comment -

                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.

                Show
                robofjoy Robert Reid added a comment - 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.
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                robofjoy Robert Reid added a comment -

                I submitted this again.
                I am closing the ticket!

                We will generate a new ticket if needed.

                Show
                robofjoy Robert Reid added a comment - I submitted this again. I am closing the ticket! We will generate a new ticket if needed.
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                robofjoy Robert Reid added a comment -

                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

                Show
                robofjoy Robert Reid added a comment - 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

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                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
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                    Dates

                    • Created:
                      Updated:
                      Resolved: