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hputnam / Geoduck_Meth

DNA methylation of geoduck exposed to ocean acidification treatments
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Obtain protein fasta files and run Orthofinder #23

Open hputnam opened 4 years ago

hputnam commented 4 years ago

obtain files for P. generosa R. philippinarum C. virginica C. gigas

Run Orthofinder on Bluewaves

sr320 commented 4 years ago

Protein Files - C. gigas https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/29159/102/GCF_902806645.1_cgigas_uk_roslin_v1/GCF_902806645.1_cgigas_uk_roslin_v1_protein.faa.gz C. virginica https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/022/765/GCF_002022765.2_C_virginica-3.0/GCF_002022765.2_C_virginica-3.0_protein.faa.gz R phil ???? (https://www.ncbi.nlm.nih.gov/assembly/GCA_009026015.1/) P gen https://osf.io/6x7p4/

hputnam commented 4 years ago

https://davidemms.github.io/

hputnam commented 4 years ago

R phil proteins??? from this publication https://academic.oup.com/gbe/article/9/6/1487/3824763#88988613 The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum) Seyoung Mun, Yun-Ji Kim, Kesavan Markkandan, Wonseok Shin, Sumin Oh, Jiyoung Woo, Jongsu Yoo, Hyesuck An, Kyudong Han Author Notes Genome Biology and Evolution, Volume 9, Issue 6, June 2017, Pages 1487–1498, https://doi.org/10.1093/gbe/evx096

NO, THESE ARE ONLY "To investigate the C1q domain copies in R. philippinarum and C. gigas genomes, we performed multiple sequence alignment with C1q Pfam seed alignments (PF00386; Finn et al. 2016). A total of 1,589 C1qDC genes including C1q seed sequences were implicated in amino acid sequence alignment analysis"

shellywanamaker commented 3 years ago

posting manila genome/transcriptome data from Mun et al. 2017 GBE here in addition to the Slack channel so it doesn't get lost:

https://drive.google.com/drive/folders/15ey7PGjnjDZeFylgXtqbnPgW_ZjLFcKm?usp=sharing