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added a lineabreak in the list
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sztankatt committed Mar 29, 2022
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9 changes: 9 additions & 0 deletions docs/tutorials/process_single_cell_data.rst
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Expand Up @@ -151,14 +151,23 @@ The results of the analysis for this sample will be under ``projects/test_projec
Under this directory, there are several files and directories which are important:

* ``final.polyA_adapter_trimmed.bam``: final, mapped, tagged ``.bam`` file. ``CB`` tag contains the cell barcode, and the ``MI`` contains the UMI-s.

* ``qc_sheet_test_sample_no_spatial_data.html``: the QC-sheet for this sample, as a self-contained ``.html`` file.

* ``dge/``: a directory containing the Digital Expression Matrices (DGEs)

* ``dge.all.polyA_adapter_trimmed.5000_beads.txt.gz``: a compressed, text based DGE

* ``dge.all.polyA_adapter_trimmed.5000_beads.h5ad``: the same DGE but stored in ``.h5ad`` format (`used by the anndata python package <https://github.com/theislab/anndata/issues/180>`_). This matrix is stored as a Compressed Sparse Column matrix (using `scipy.sparse.csc_matrix <https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.csc_matrix.html>`_).

* ``dge.all.polyA_adapter_trimmed.5000_beads.summary.txt``: the summary of the DGE, one line per cell.

* ``dge.all.polyA_adapter_trimmed.5000_beads.obs.csv``: the observation table of the matrix. Similar to the previous file, more detailed.

* ``automated_analysis/test_run_mode/umi_cutoff_50/``: In this directory the results of the automated analysis can be found. As it can be seen under the ``automated_analysis`` directory there are two further levels, one for ``run_mode`` and one for ``umi_cutoff``. This is because one sample can have several ``run_modes`` and in the same way one ``run_mode`` can have several UMI cutoffs.

* ``results.h5ad``: the result of the automated analysis, stored in an anndata object. Same as the DGE before, but containing processed data.

* ``test_sample_no_spatial_data_illumina_automated_report.html``: automated analysis self-contained ``.html`` report.

.. note::
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