Changes between Version 55 and Version 56 of SOPs/qc_shortReads


Ignore:
Timestamp:
10/20/20 13:05:28 (4 years ago)
Author:
gbell
Comment:

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  • SOPs/qc_shortReads

    v55 v56  
    8282The "Basic Statistics" section at the top of the FastQC report also shows the Encoding (quality score) information (like "Illumina 1.5"), which may be necessary to specify in subsequent analysis steps.  The Encoding scales are described at [http://en.wikipedia.org/wiki/FASTQ_format#Encoding].
    8383
     84== MultiQC ==
     85
     86[[https://multiqc.info/|MultiQC]] is a program that can merge QC and other reports (such as FastQC, STAR, and MACS2) for a series of samples into one big file.  See [[https://multiqc.info/#supported-tools|MultiQC: Supported Tools]] for a table of about 100 types of reports that can be merged.
     87
     88The main command to merge reports in your current directory is
     89{{{
     90# Usage: multiqc [OPTIONS] <analysis directory>
     91multiqc -n My_samples.reports.html .
     92}}}
     93Note the " .", which indicates the current directory.  Otherwise, a series of directories can be used as arguments.
    8494
    8595== QC for paired-end reads ==