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| − | =Introduction=
| + | No Name [/home/nutria], b1, wiki |
| − | | + | |Introduction |
| − | Assessment of short read quality
| + | |FastQC |
| − | | + | = . |fastqc's help file |
| − | =MultiQC =
| + | |MultiQC |
| − | | + | |multiqc's help file |
| − | A relatively new tool that aggregates the output of FASTQC into one report.
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| − | | |
| − | * available on the command line with any module loading as it is a python module (already installed easily via pip)
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| − | | |
| − | Go into the directory where the FASTQC output is and run
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| − | multiqc . | |
| − | | |
| − | the dot stands for the local directory, and is obligatory.
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| − | | |
| − | Under its general statistics we get the following headings:
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| − | | |
| − | * Sample Name
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| − | * % Dups
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| − | * % GC
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| − | * Length
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| − | * M Seqs, millions of sequences
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| − | | |
| − | = multiqc's help file =
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| − | | |
| − | Usage: multiqc [OPTIONS] <analysis directory>
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| − |
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| − | MultiQC aggregates results from bioinformatics analyses across many
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| − | samples into a single report.
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| − |
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| − | It searches a given directory for analysis logs and compiles a HTML
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| − | report. It's a general use tool, perfect for summarising the output from
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| − | numerous bioinformatics tools.
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| − |
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| − | To run, supply with one or more directory to scan for analysis results.
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| − | To run here, use 'multiqc .'
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| − |
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| − | See http://multiqc.info for more details.
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| − |
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| − | Author: Phil Ewels (http://phil.ewels.co.uk)
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| − |
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| − | Options:
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| − | -f, --force Overwrite any existing reports
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| − | -d, --dirs Prepend directory to sample names
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| − | -s, --fullnames Do not clean the sample names (leave as full
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| − | file name)
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| − | -i, --title TEXT Report title. Printed as page header, used
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| − | for filename if not otherwise specified.
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| − | -n, --filename TEXT Report filename. Use 'stdout' to print to
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| − | standard out.
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| − | -o, --outdir TEXT Create report in the specified output
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| − | directory.
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| − | -t, --template [default|default_dev|geo|simple]
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| − | Report template to use.
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| − | -x, --ignore TEXT Ignore analysis files (glob expression)
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| − | -e, --exclude [module name] Do not use this module. Can specify multiple
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| − | times.
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| − | -m, --module [module name] Use only this module. Can specify multiple
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| − | times.
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| − | --data-dir / --no-data-dir Specify whether the parsed data directory
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| − | should be created.
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| − | -k, --data-format [tsv|yaml|json]
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| − | Output parsed data in a different format
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| − | -z, --zip-data-dir Compress the data directory.
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| − | --flat Use only flat plots (static images)
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| − | --interactive Use only interactive plots (HighCharts
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| − | Javascript)
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| − | -c, --config PATH Specific config file to load, after those in
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| − | MultiQC dir / home dir / working dir.
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| − | -v, --verbose Increase output verbosity.
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| − | -q, --quiet Only show log warnings
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| − | --version Show the version and exit.
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| − | -h, --help Show this message and exit.
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| − | | |
| − | | |
| − | = fastqc's help file =
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| − | | |
| − | SYNOPSIS
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| − |
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| − | fastqc seqfile1 seqfile2 .. seqfileN
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| − |
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| − | fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam] [-c contaminant file] seqfile1 .. seqfileN
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| − |
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| − | DESCRIPTION
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| − |
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| − | FastQC reads a set of sequence files and produces from each one a quality
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| − | control report consisting of a number of different modules, each one of
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| − | which will help to identify a different potential type of problem in your
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| − | data.
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| − |
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| − | If no files to process are specified on the command line then the program
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| − | will start as an interactive graphical application. If files are provided
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| − | on the command line then the program will run with no user interaction
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| − | required. In this mode it is suitable for inclusion into a standardised
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| − | analysis pipeline.
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| − |
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| − | The options for the program as as follows:
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| − |
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| − | -h --help Print this help file and exit
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| − |
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| − | -v --version Print the version of the program and exit
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| − |
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| − | -o --outdir Create all output files in the specified output directory.
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| − | Please note that this directory must exist as the program
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| − | will not create it. If this option is not set then the
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| − | output file for each sequence file is created in the same
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| − | directory as the sequence file which was processed.
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| − |
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| − | --casava Files come from raw casava output. Files in the same sample
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| − | group (differing only by the group number) will be analysed
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| − | as a set rather than individually. Sequences with the filter
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| − | flag set in the header will be excluded from the analysis.
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| − | Files must have the same names given to them by casava
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| − | (including being gzipped and ending with .gz) otherwise they
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| − | won't be grouped together correctly.
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| − |
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| − | --nofilter If running with --casava then don't remove read flagged by
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| − | casava as poor quality when performing the QC analysis.
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| − |
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| − | --extract If set then the zipped output file will be uncompressed in
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| − | the same directory after it has been created. By default
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| − | this option will be set if fastqc is run in non-interactive
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| − | mode.
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| − |
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| − | -j --java Provides the full path to the java binary you want to use to
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| − | launch fastqc. If not supplied then java is assumed to be in
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| − | your path.
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| − |
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| − | --noextract Do not uncompress the output file after creating it. You
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| − | should set this option if you do not wish to uncompress
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| − | the output when running in non-interactive mode.
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| − |
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| − | --nogroup Disable grouping of bases for reads >50bp. All reports will
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| − | show data for every base in the read. WARNING: Using this
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| − | option will cause fastqc to crash and burn if you use it on
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| − | really long reads, and your plots may end up a ridiculous size.
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| − | You have been warned!
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| − |
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| − | -f --format Bypasses the normal sequence file format detection and
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| − | forces the program to use the specified format. Valid
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| − | formats are bam,sam,bam_mapped,sam_mapped and fastq
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| − |
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| − | -t --threads Specifies the number of files which can be processed
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| − | simultaneously. Each thread will be allocated 250MB of
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| − | memory so you shouldn't run more threads than your
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| − | available memory will cope with, and not more than
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| − | 6 threads on a 32 bit machine
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| − |
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| − | -c Specifies a non-default file which contains the list of
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| − | --contaminants contaminants to screen overrepresented sequences against.
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| − | The file must contain sets of named contaminants in the
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| − | form name[tab]sequence. Lines prefixed with a hash will
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| − | be ignored.
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| − |
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| − | -a Specifies a non-default file which contains the list of
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| − | --adapters adapter sequences which will be explicity searched against
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| − | the library. The file must contain sets of named adapters
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| − | in the form name[tab]sequence. Lines prefixed with a hash
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| − | will be ignored.
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| − |
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| − | -l Specifies a non-default file which contains a set of criteria
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| − | --limits which will be used to determine the warn/error limits for the
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| − | various modules. This file can also be used to selectively
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| − | remove some modules from the output all together. The format
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| − | needs to mirror the default limits.txt file found in the
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| − | Configuration folder.
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