QuickStart 

Required data formats

There are few specifc requirements for the input data for PipeCraft.

Paired-end data
- must contain **R1** and **R2** strings in the paired-end files,
- sample names maynot contain ‘R1/R2’ strings
  
  OK file names: my_sample_01_R1_L001.fastq and my_sample_01_R2_L001.fastq
  
  NOT-OK file names: my_R1sample_01_R1_L001.fastq and my_R1sample_01_R2_L001.fastq or my_sample_01_1.fastq and my_sample_01_2.fastq
index/barcodes file for demultiplexing:
- see formatting requirements here
specific directory structure of NextITS pipeline
- see NextITS page here

How to START

1. To START any analyses, you must specify the working directory (WORKDIR) by pressing the SELECT WORKDIR button. E.g., if working with fastq files, then be sure that the working directory contains only relevant fastq files because the selected process will be applied to all fastq files in the working directory!

Note

When using Windows OS, the selection window might not display the files while browsing through the directories.

After selecting a working directory, PipeCraft needs you to specify if

if the data is paired-end or single-end

and the extension of the data (fastq or fasta)

paired-end data –> such as data from Illumina or MGI-Tech platforms (R1 and R2 files). Be sure to have **R1** and **R2** strings in the paired-end files (not simply _1 and _2; and sample names maynot contain R1/R2 strings)

single-end data –> such as data from PacBio, or assembled paired-end data (single file per library or per sample)

2. SELECT PIPELINE or press Quick Tools button to select relevant step; edit settings if needed and start running the analyses by pressing the START button.

Note

When running ‘step-by-step analyses with Quick Tools’: when one workflow is finished, then press SELECT WORKDIR to specify inputs for the next process to ensure the correct workflow piping.

Warning

The outputs will be overwritten if running the same analysis step multiple times in the same working directory. If needed, edit the default output directory name to prevent that.

Each process creates a separate output directory with the processed files. The README file in the output directory states some of the details about the finished process.

Ready-to-run pre-defined pipelines here

QuickTools page here

Quality scores and basic statistics screening of the data

Quality and basic statistics screening of the data can be done via QualityCheck panel. QualityCheck panel implements FastQC and MultiQC to screen the input fastq files.

To start:

Select folder (a working directory) which contains only fastq (fastq/fq) files that you aim to inspect.

Press CREATE REPORT to start MultiQC

“LOADING …” will be displayed while the report is being generated

Click VIEW REPORT. A html file (multiqc_report.html) will open in your default web browser.

If the summary does not open, check your working floder for the presence of multiqc_report.html and try to open with some other web browser. Something went wrong if the file multiqc_report.html does not exist (may fail when maximum number of fastq files in the folder is extremely large, >10 000).

Check out “using MultiQC reports” in MultiQC web page.

Note

Note that ‘_fastqc.zip’ and ‘_fastqc.html’ are generated for each fastq file in the ‘quality_check’ directory. These are summarized in multiqc_report.html, so you may delete all individual ‘_fastqc.zip’ and ‘_fastqc.html’ files if those are of no interest.