.. _config-multiome:

Multiome Examples
=================

Below are different examples of setting up workflows for Multiome 
experiments. For general configuration details, see :ref:`config`.


Multiple samples
----------------

.. code-block::
    :caption: samples.tsv

    sample      replicate genome HDF5_Multiple_Assays                           RDS_Multiple_Assays Gene.Expression   Peaks   TF  fragments                              singlecell meta_batch  meta_geno
    rep1_wt               mm10   rep1_wt/outs/filtered_feature_bc_matrix.h5                                                       rep1_wt/outs/atac_fragments.tsv.gz                batch1      wt
    rep1_homo             mm10   rep_homo/outs/filtered_feature_bc_matrix.h5                                                      rep1_homo/outs/atac_fragments.tsv.gz              batch1      ko


Multiple samples, aggregated
----------------------------

.. code-block::
    :caption: samples.tsv

    sample      replicate       genome  HDF5_Multiple_Assays                    RDS_Multiple_Assays     Gene.Expression Peaks   TF      fragments                       singlecell      meta_batch
    multiome                    mm10    rep1/outs/filtered_feature_bc_matrix.h5                                                         rep1/outs/atac_fragments.tsv.gz                 batch1

.. code-block::
    :caption: aggregates.tsv

    sample  replicate library_id library_id meta_geno
    rep1_wt           1          1          wt
    rep1_ko           2          2          ko


Technical Replicates (Uncommon)
-------------------------------

.. code-block::
    :caption: samples.tsv

    sample replicate genome HDF5_Multiple_Assays                     RDS_Multiple_Assays Gene.Expression   Peaks   TF  fragments                        singlecell    meta_batch  meta_geno
    pbmc1  A         hg38   pbmc1/outs/filtered_feature_bc_matrix.h5                                                   pbmc1/outs/atac_fragments.tsv.gz               batch1      wt
    ipsc   A         hg38   ipsc/outs/filtered_feature_bc_matrix.h5                                                    ipsc/outs/atac_fragments.tsv.gz                batch2      wt
    pbmc2  A         hg38   pbmc2/outs/filtered_feature_bc_matrix.h5                                                   pbmc2/outs/atac_fragments.tsv.gz               batch2      wt
    pbmc1  B         hg38   pbmc1/outs/filtered_feature_bc_matrix.h5                                                   pbmc1/outs/atac_fragments.tsv.gz               batch1      wt
    ipsc   B         hg38   ipsc/outs/filtered_feature_bc_matrix.h5                                                    ipsc/outs/atac_fragments.tsv.gz                batch2      wt
    pbmc2  B         hg38   pbmc2/outs/filtered_feature_bc_matrix.h5                                                   pbmc2/outs/atac_fragments.tsv.gz               batch2      wt


Custom assays (Uncommon)
------------------------

.. code-block::
    :caption: samples.tsv

    sample replicate genome HDF5_Multiple_Assays                     RDS_Multiple_Assays Gene.Expression   Peaks   TF  fragments                        singlecell  meta_batch  meta_geno
    pbmc1            hg38   pbmc1/outs/filtered_feature_bc_matrix.h5                                                   pbmc1/outs/atac_fragments.tsv.gz             batch1      wt
    ipsc             hg38   ipsc/outs/filtered_feature_bc_matrix.h5                                                    ipsc/outs/atac_fragments.tsv.gz              batch2      wt
    pbmc2            hg38   pbmc2/outs/filtered_feature_bc_matrix.h5                                                   pbmc2/outs/atac_fragments.tsv.gz             ratch2      wt

.. code-block::
    :caption: assays.tsv

    sample replicate assay.name path
    pbmc1
    ipsc             enhancer   pbmc1/assays/enhancer_bc_matrix.h5
    pbmc1