🍻
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
Powered by GitBook
On this page
  • How to check whether you are in the mapping environment?
  • Why using a conda environment?
  • What is the PlateInfo file?
  • What is the MappingConfig file?
  • What is Snakemake?
  • What is netCDF4?

Was this helpful?

  1. Other

FAQ

How to check whether you are in the mapping environment?

# when I login to server, my default python is in miniconda3/bin, 
# the base environment
$ which python
~/work/miniconda3/bin/python
(base)

# entering the mapping environment
$ conda activate mapping

# now I check the path of python again, it changed to my env dir
$ which python
~/work/miniconda3/envs/mapping/bin/python
(mapping)

# packages installed for mapping env all located at 
# ~/work/miniconda3/envs/mapping

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?

  • Briefing on INI format:

    ; comment start with semicolon
    [section1]
    key1=value1
    key2=value2
    
    [section2]
    key1=value1
    key2=value2
  • Currently, the pipeline doesn’t allow you to change the sections and keys, so just change values according to your needs.

What is Snakemake?

What is netCDF4?

PreviousMethylome Pseudo-bulkNextChangelog

Last updated 4 years ago

Was this helpful?

It contains all the parameters of the mapping pipeline in

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).

INI format
Snakemake