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usage.md

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Useage

The pipeline may be started by passing LowPassKaryo_Wrapper.R to Rscript with one or two command line parameters, e.g.

Rscript LowPassKaryo_Wrapper.R --help

The principal useage though will be to provide a design file:

Rscript LowPassKaryo_Wrapper.R --design lowpass_design_file.txt

The design file should be a tab separated text file consisting of two sections:

A two column header containing

  1. A name for the project/run
  2. The directory containign the FastQ files
  3. The base working directory - a sub-directory will be created using the project name and results and temporary files will be created here.
  4. Optional Scheduler parameters - entries other than NA here will over-ride (i.e. completely replace) the existing defaults. (Column 1 contains the variable tags Column 2 contains the values)

Following this is a four column table with one row per sample and the following columns

  1. ##LIMS_ID - A unique identifier for this sample corresponding to the first underscore separated field of the fastq files names. e.g. for NGS1234_S26_L005_R1_001.fastq.gz the LIMS_ID would be NGS1234
  2. ##SAMPLE_NAME - a descriptive name for the sample, e.g. WildType-Time0-Replicate1
  3. ##GENOME_TAG - which genome should the sample be aligned to. The entries here should correspond to the "Tag" entries of the genome_lookup_table.txt
  4. ##ANNO_BED - an optional bed file indicating regions of interest to be annotated in the logR plots. Set to NA to skip annotation.

A template design file indicating the expected format can be generated as follows

Rscript LowPassKaryo_Wrapper.R ----template-design