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Remove ORF sequences from SONARRamesh rhesus germline set #72

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ressy opened this issue Mar 22, 2024 · 0 comments
Open

Remove ORF sequences from SONARRamesh rhesus germline set #72

ressy opened this issue Mar 22, 2024 · 0 comments
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enhancement New feature or request

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@ressy
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ressy commented Mar 22, 2024

I'd originally left rhesus germline V genes with the "ORF" prefix in place as SONAR has them, but I should probably remove them. IgDiscover will very occasionally detect (technically correctly, as far as I can tell, based on the removed introns) transcribed antibody recombinations for V genes labeled non-functional ORFs in Ramesh et al. 2017's rhesus reference, but, these are still presumably non-functional from a protein standpoint, so we'd rather not have them reported in the output. The names also cause trouble for some of SONAR's parsing code. Removing them would make the germline sequences here consistently limited to functional cases.

ORF_IGHV3-AHA-X*01
ORF_IGHV3-AHG-X*01
ORF_IGHV3-AHH-X*01
ORF_IGKV1-AES-X*01
ORF_IGKV2-AEQ-X*01
ORF_IGKV2-AET-X*01
ORF_IGKV2-AET-X*03
ORF_IGKV2-AET-X*04
ORF_IGLV7-ADJ*01
ORF_IGLV7-ADJ*02
ORF_IGLV8-AEE-X*01
ORF_IGLV8-AEE-X*02
ORF_IGLV8-AEE-X*03
@ressy ressy added the enhancement New feature or request label Mar 22, 2024
@ressy ressy added this to the 0.6.0 milestone Mar 22, 2024
@ressy ressy removed this from the 0.6.0 milestone May 17, 2024
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