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[SUGGESTION] Take 10x Multiome data as inputs #351

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cflerin opened this issue Jul 23, 2021 · 0 comments
Open

[SUGGESTION] Take 10x Multiome data as inputs #351

cflerin opened this issue Jul 23, 2021 · 0 comments
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enhancement New feature or request

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@cflerin
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cflerin commented Jul 23, 2021

Is your feature request related to a problem? Please describe.
I need to import RNA and ATAC data from Cell Ranger ARC outs/.

Describe the solution you'd like
getDataChannel should return separate channel entries for the data present in outs/, linked by sampleID, and having a different key describing the data type:

  • RNA:
    • [ sampleId, path/to/outs/filtered_feature_bc_matrix/*, 10x_mo_cellranger_mex_rna, ..., ... ]
  • ATAC:
    • [ sampleId, [ outs/atac_possorted_bam.bam, outs/atac_possorted_bam.bam.bai], bam, ..., ...]
    • [ sampleId, [ outs/atac_fragments.tsv.gz, outs/atac_fragments.tsv.gz.tbi], fragments, ..., ...]

Describe alternatives you've considered
Use the standard tenx profile and process this channel afterward to extract these files. This might even be preferable, as it would limit the choices of input data profiles. There could be a 'translation' function to go from this input type to the ones listed above.

Additional context
N/A

@cflerin cflerin added the enhancement New feature or request label Jul 23, 2021
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