FAQ

How to check whether you are in the mapping environment?

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# when I login to server, my default python is in miniconda3/bin,
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# the base environment
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$ which python
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~/work/miniconda3/bin/python
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(base)
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# entering the mapping environment
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$ conda activate mapping
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# now I check the path of python again, it changed to my env dir
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$ which python
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~/work/miniconda3/envs/mapping/bin/python
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(mapping)
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# packages installed for mapping env all located at
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# ~/work/miniconda3/envs/mapping
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Why using a conda environment?

  • Using environment make sure all the mapping related package is handled by conda and pip in a stand-alone place.
  • It will not impact any of your other installed packages and vise versa.
  • The only drawback of using the environment is you need to activate the environment every time. Because everything is only installed for that environment.

What is the PlateInfo file?

  • A plain text file with experimental, library, and barcoding information.
  • This file needs to be made manually for each library.
  • The main content of this file is the PCR index information for each plate in the library, so the pipeline can properly demultiplex and name the raw FASTQ files with that information.

What is the MappingConfig file?

  • It contains all the parameters of the mapping pipeline in INI format
  • Briefing on INI format:
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    ; comment start with semicolon
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    [section1]
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    key1=value1
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    key2=value2
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    [section2]
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    key1=value1
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    key2=value2
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  • Currently, the pipeline doesn’t allow you to change the sections and keys, so just change values according to your needs.

What is Snakemake?

Snakemake is a package for writing a reproducible pipeline. It uses Snakefile to describe all steps of a pipeline. During demultiplex, I prepared this file for you and saved it in each of the subdirectories. All you need to do is execute these files (via snakemake, commands also summarized during demultiplexing).

What is netCDF4?