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spatula eval-dups-sbcds

Summary

spatula eval-dups-sbcds examines duplicates in the spatial barcode dictionary generated by spatula build-sbcds and produces summary statistics.

Here is a summary of the main features:

  • Input: Takes a spatial barcode directory from build-sbcds.
  • Output: In the output directory, it produces (a) a complete list of duplicate barcodes, with the number of occurrences and the number of unique tiles observed, (b) per-tile summary metrics of the number of duplicate barcodes, and © the histogram of the observed counts of each duplicate.

An example use of the tool is as follows:

spatula eval-dups-sbcds --sbcd /path/to/sbcd/dir/ \
                        --out  /path/to/output_prefix
See below for a more detailed usage description.

Required options

  • --sbcd : The path to the directory containing spatial barcode files, generated by build-sbcds.
  • --out : The prefix for the output files. See Expected Output for more details.

Additional options

  • --match-len : The length of the spatial barcode to consider for a match. The default is 27, and the maximum possible value is 27.

Expected Output

With [out_prefix] as the prefix, the following files will be created:

  • [out_prefix].dups.sbcds.tsv.gz : A compressed tsv file containing the following entries in each line:
    • barcode : Spatial barcode that is observed multiple times across the tiles.
    • ntiles : Number of unique tiles where the spatial barcodes were observed.
    • dupcount : The number of occurrences of the spatial barcode across the tiles.
  • [out_prefix].tiles.tsv : A tab-delimited file summarizing the duplicate barcode statistics. It contains the following entries in each row:
    • tile : The ID of the tile, in the format of lane_tile.
    • total : The total number of spatial barcodes found in the tile.
    • uniq : The number of unique spatial barcodes (across tiles) found in the tile.
    • dups_uniq : The number of non-unique spatial barcodes in the tile, counting only once per tile.
    • dups_within : The number of non-unique spatial barcodes observed only within a single tile, counting only once per tile.
    • dups_between : The number of non-unique spatial barcodes observed across multiple tiles, counting only once per tile.
  • [out_prefix].hist.tsv : The histogram of the observed counts of each duplicate, across all tiles. It contains the following entries in each row.
    • dupcount : The number of occurrences of the spatial barcode across the tiles.
    • num : The number of spatial barcodes observed with the dupcount occurrences.

Full Usage

The full usage of the software tool is as follows:

$ ./spatula eval-dups-sbcds --help
[./spatula eval-dups-sbcds] -- Evaluate duplicates in spatial barcodes

 Copyright (c) 2022-2024 by Hyun Min Kang
 Licensed under the Apache License v2.0 http://www.apache.org/licenses/

Detailed instructions of parameters are available. Ones with "[]" are in effect:

Available Options:

== Input options ==
   --sbcd      [STR: ]             : Spatial barcode dictionary generated from 'build-sbcds' command
   --match-len [INT: 27]           : Length of HDMI spatial barcodes to require perfect matches

== Output Options ==
   --out       [STR: ]             : Prefix of output files (.dups.sbcds.tsv.gz, .tiles.tsv, .hist.tsv)


NOTES:
When --help was included in the argument. The program prints the help message but do not actually run