> For the complete documentation index, see [llms.txt](https://hq-1.gitbook.io/mc/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://hq-1.gitbook.io/mc/other/faq.md).

# 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?

* It contains all the parameters of the mapping pipeline in [INI format](https://en.wikipedia.org/wiki/INI_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?

[Snakemake](https://snakemake.github.io/) 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?


---

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