hubmapconsortium / search-api

HuBMAP search service and associated pieces to create an index
https://search.api.hubmapconsortium.org
MIT License
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Fix names for SNARE #184

Closed mccalluc closed 4 years ago

mccalluc commented 4 years ago

Chris emailed with Blue Lake and came to this conclusion:

FYI, Blue has clarified how Snare RNAseq & ATACseq should be classified. In short:

They both are single nucleus assays, but for ATAC the assay is referred to as scATAC-seq (10X scATAC-seq also involves nuclei)

SNARE-seq2 has 2 components : SNARE-RNAseq should be under snRNA-seq & SNARE-ATACseq should be under scATAC-seq

mccalluc commented 4 years ago

These are the terms in assay-types.yaml which include SNARE:

SNAREseq:
    description: SNARE-seq
salmon_rnaseq_snareseq:
    description: scRNA-seq (SNARE-seq) [Salmon]
sc_atac_seq_snare:
    description: scATAC-seq (SNARE-seq) [SnapATAC]
sc_rna_seq_snare_lab:
    description: scRNA-seq (SNARE-seq) [Lab Processed]
sc_atac_seq_snare_lab:
    description: scATAC-seq (SNARE-seq) [Lab Processed]

@cebriggs7135 : Can you make a PR, from the devel branch, with the changes? Or can you state precisely what these lines should be changed to, and I'll make the PR?

cebriggs7135 commented 4 years ago

Here's a link https://drive.google.com/file/d/1cQYx0_nM4aYeFjnpCaQVPlxL2e0nJwHZ/view?usp=sharing to a pdf of that email exchange with Blue about :

versus