Details
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Type: Task
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Status: Closed (View Workflow)
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Priority: Minor
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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:Summer 4 2023 June 26
Description
Situation: The most recent rat genome (rn7) is not currently available in IGB.
Task: Add the rn7 rat genome to IGB: https://hgdownload.soe.ucsc.edu/downloads.html#rat
Attachments
Issue Links
- relates to
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IGBF-3330 Add mm39 (GRCm39) mouse genome to IGB
- Closed
I downloaded the Nov. 2020 (mRatBN7.2/rn7) assembly of the rat genome (rn7) 2bit file from https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/
I pulled the rat info from gene2accession file using NCBI txid 10116
I created bed 14 files for UCSC refGene and NCBI Ref Seq (ncbiRefSeq):
I then sorted, bgzipped, and tabix indexed the two bed files:
Next I sorted, bgzipped, and tabix indexed the psl files for all_est and all_mrna: