Skip to content

Latest commit

 

History

History
60 lines (40 loc) · 3.16 KB

README.md

File metadata and controls

60 lines (40 loc) · 3.16 KB

Configuration

Before using the pipeline the following files need to be provided/adapted:

  1. config.yaml
  2. samplemap
  3. HashingFile
  4. featureReferenceFile

config.yaml

Before running the pipeline the config.yaml file needs to be adapted to contain the input and output paths for the intended analysis.

Adaptation necessary for a default run:

  • In section [inputOutput] the input directories input_fastqs_gex, input_fastqs_adt need to point to the location of the respective FASTQ files. This location needs to be specified relative to the gExcite working directory (usually gExcite_pipeline/).
  • In section [resources], reference_transcriptome needs to point to the location of the genomic reference used for the cellranger mapping
  • In sections [tools][cellranger_count_gex] and [tools][cellranger_count_adt], call needs to point to the the path to the cellranger installation
  • Section [computingResources] needs to list the resources that can be assigned to the analysis steps your data and batch system. The example resources specify memory per job, not thread.
  • Section [scampi][resources] needs to be filled with the cell type information, selected genes to show in expression plots, and gene sets for the GSVA analysis.

The default example config file is pointing to the example data input files.

samplemap

Further, a "samplemap" must be provided specifying sample-specific parameters in a tab-delimited text file. A pre-configured samplemap ready to run on the test data that can be adapted is provided in this directory.

Example samplemap:

sample    HashingFile     nTargetCells    featureReferenceFile
sampleA   HashingFileA    10000           featureReferenceFileA
sampleB   HashingFileB    15000           featureReferenceFileB

With one line per set of samples

  • sample contains the sample identifier that is used throughout the pipeline

  • HashingFile contains the full path to the comma separated text file containing the hashtag barcodes and their assignment to individual sample names (see HashingFile).

  • nTargetCells corresponds to the number of targeted cells for the sample.

  • featureReferenceFile corresponds to the ADT feature reference file for the sample set. For further information please consult the Cellranger tool documentation.
    NOTE: the path to the FeatureReferenceFile must be relative to the gExcite working directory (usually gExcite_pipeline/).

HashingFile

In case of hashed samples, the hashtag barcodes, the hashtag names, and the corresponding sample names must be associated with the sample set. To do so, we need a comma-separated file with the following structure:

Barcode1,TagName1,sampleA
Barcode2,TagName2,sampleB

 featureReferenceFile

The "featureReferenceFile" is a comma-separated text file describing all ADT antibodies used in the experiment at hand. For further information please consult the Cellranger tool documentation.
An example feature_reference.txt ready to run on the test data is available in the testdata directory.