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YAP
  • Before Start
  • Installation
  • TECH BACKGROUND
    • Barcoding
    • Technology References
    • File Formats
  • Mapping Pipeline
  • Prepare
    • Prepare PlateInfo & bcl2fastq SampleSheet
    • Prepare Mapping Config
      • Prepare Reference Files
  • Demultiplex
  • Mapping
    • Mapping Via Qsub
    • Mapping Via Sbatch
    • Mapping Locally
  • Mapping Form Cell-Level FASTQ Files
  • Summary
  • Mapping Metrics
    • Key Mapping Metrics
    • All Mapping Metrics
  • Generate MCDS
  • Pseudo-bulk
    • Methylome Pseudo-bulk
  • Other
    • FAQ
    • Changelog
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On this page
  • Input
  • Cell batches and snakemake
  • Execute snakemake commands
  • For MiSeq
  • For NovaSeq
  • For troubleshooting

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Mapping

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Last updated 4 years ago

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Input

  • yap demultiplex output directory, refer to as {output_dir} below.

Cell batches and snakemake

During demultiplex, cells are divided into small batches based on their PCR index. FASTQ files of each batch are saved together in a sub-directory of the {output_dir} . Each of the sub-directory is mapped together in a single job, all the steps that need to be done are written in the {output_dir}/{sub_dir}/Snakefile , a file needed by , and contain all the commands to map the files in this sub-directory.

Here is a single command used to execute the Snakefile, but you don't need to do this by yourself (see below):

# to map cells in a single sub directory

snakemake \
-d {output_dir}/{sub_dir} \
--snakefile {output_dir}/{sub_dir}/Snakefile \
-j {parallel_cores_to_use_for_this_job}

Execute snakemake commands

In the {output_dir}/snakemake , you should be able to find a list of snakemake commands like the above, one command for each PCR index sub-directory. You have three ways to execute these commands.

For MiSeq

For NovaSeq

For troubleshooting

Mapping Via Qsub
Mapping Via Sbatch
Mapping Locally
snakemake
What is snakemake?