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  1. IGB
  2. IGBF-4345

m6A pipeline one more time!

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

          GOAL: To run the m6a PIpeline again with the hope of finding sites in the 3' UTR region.

          Kausik had his grad student produce more DART seq data.

          https://drive.google.com/drive/folders/1Q_RjN1kX5jXxfNbKzPs9ErIMsE5aSf3M?usp=sharing

          Data going onto the cluster location =
          /projects/chakrabartilab/fnb0/plasmodium/dart2

          The end desire of finding m6a sites in those 3'UTR regions.....

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              bbendick Brandon Bendickson added a comment - - edited

              Wait for Dr. Reid's Bullseye run before proceeding.

              Pipeline steps:
              1. Align new sequences with BWA-Mem: Done
              2. Convert new Bams to Beds: Done
              3. Write script that does the following:

              • Read in Pfalciparum fasta (forward/reverse)
              • Read in new bed file into a list of lists [(chromosome, align start, align end, strand), ...]
              • read and parse 3' Pfalciparum gff file and store Chromsome, UTR start, UTR end, GeneID, and strand
              • Using 3' UTR coords, pull the sequenced of those portions from fasta
              • If the alignment start falls into the UTR range, save all associated data/sequences
              • Manually search matched 3' region sequences for m6A RAC motif and record coords.
                4. Iterate for all beds
                5. Share results
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              bbendick Brandon Bendickson added a comment - - edited Wait for Dr. Reid's Bullseye run before proceeding. Pipeline steps: 1. Align new sequences with BWA-Mem: Done 2. Convert new Bams to Beds: Done 3. Write script that does the following: Read in Pfalciparum fasta (forward/reverse) Read in new bed file into a list of lists [(chromosome, align start, align end, strand), ...] read and parse 3' Pfalciparum gff file and store Chromsome, UTR start, UTR end, GeneID, and strand Using 3' UTR coords, pull the sequenced of those portions from fasta If the alignment start falls into the UTR range, save all associated data/sequences Manually search matched 3' region sequences for m6A RAC motif and record coords. 4. Iterate for all beds 5. Share results

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                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
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                  • Created:
                    Updated:
                    Resolved: