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  1. IGB
  2. IGBF-4215

Mapping SolyID to Kegg by way of RefSEq / NCBI via BLAST

        Details

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

          Description

          So the problem is that with KEGG as we currently stand,

          we only have 4000 KEGG ids that map to about 8700 SL4 genes.

          Since there are 34,000 genes, we are leaving MANY genes out of consideration.

          However, there is a KEGG API mapping file that associates NCBI Ids for tomato to KEGG IDs. (see attached)

          Looks like so:
          100037489 NP_001234263
          100037490 NP_001234268
          100037491 NP_001234273
          100037492 NP_001234279
          100037493 NP_001234283
          100037494 NP_001234289
          100037498 NP_001234310
          100037495 NP_001234471
          100037496 XP_004230843

          Ultimately we need a salmon counts table that is NORMALIZED !! And has a column with the KEGG ids, (1st column).

          HERE:
          Download all of the NCBI IDs from column 2.
          Blast Soly genes to these IDs and make a new table with the top hit.
          Summarize how many hits do we get, how many misses also.

            Attachments

            1. soly_mapping.tsv
              1021 kB
            2. kegg-api-sly.txt
              592 kB
            3. best_hits_kegg.tsv
              1.43 MB

              Activity

                People

                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
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                  Dates

                  • Created:
                    Updated:
                    Resolved: