Abstract

This modified version of MultiQC added modules named NuGEN_dedup and FCount_cus

• NuGEN_dedup:process the data of deduplication by using NuGEN set for the extracellular RNA project
• FCount_cus: Count the number of genes that appear 0-10 times, 10-100 times and greater then 100 times.

Modified files:

setup.py (~/MultiQC/setup.py) add

• 'NuGEN_dedup = multiqc.modules.NuGEN_dedup:MultiqcModule'
• 'FCount_cus = multiqc.modules.FCount_cus:MultiqcModule'

to the entry_points section

search_patterns.yaml (~/MultiQC/multiqc/utils/search_patterns.yaml) add search pattern to the search_patterns.yaml.

The format of output of NuGEN deduplication is _dup_log.txt The format of output of FCount_cus is .mergeCount

NuGEN_dedup:
    fn: '*_dup_log.txt'
FCount_cus"
    fn:'*.mergeCount'

config_defaults.yaml (~/MultiQC/multiqc/utils/config_defaults.yaml) add the module to the top of module_order in config_defaults.yaml

module_order:
    # MultiQC general module for catching output from custom scripts
    - 'custom_content'
    - NuGEN_dedup:
        module_tag:
            - RNA
    - FCount_cus:
        modeule_tag:
            - RNA

README.md (~/MultiQC/docs/README.md) add the information of added module NuGEN_dedup and FCount_cus to the post-alignment section of README

Post-alignment:
    NuGEN_dedup: modules/NuGEN_dedup.md
    FCount_cus: modules/FCount_cus.md

Added directory and files

.md

• NuGEN_dedup.md (~docs/modules/NuGEN_dedup.md)
• FCount_cus.md** (~docs/modules/FCount_cus.md)

added explianation file under the directory of doc. No meaningful content in this file

directory

• NuGEN_dedup (~/MultiQC/multiqc/modules/NuGEN_dedup)
• FCount_cus** (~/MultiQC/multiqc/modules/FCount_cus)

created directory under the directory of module. The name of directory should be the same as the name of module. This directory will hold the file of __init__.py and moduleName.py.

.py

• NuGEN_dedup.py (~/MultiQC/multiqc/modules/NuGEN_dedup/NuGEN_dedup.py)
• FCount.py (~/MultiQC/multiqc/modules/FCount_cus/FCount_cus.py)

The main program for add data to general stats and add section to the multiQC report. Name should be the same as the name of module

init.py

• (~/MultiQC/multiqc/modules/NuGEN_dedup/init.py)
• (~/MultiQC/multiqc/modules/FCount_cus/init.py)

import all the modules that provided by MultiQC. Also creates the entry point for our module

Cuerrent MultiQC contains following tools.