Merge pull request /issues/210 from tejashree1modak/prereq

Adding a sanity check for fastqc being installed

episodes/02-quality-control.md

@@ -190,6 +190,134 @@ very poor (`#` = a quality score of 2).
 > {: .solution}
 {: .challenge}
 
+At this point, lets validate that all the relevant tools are installed. If you are using the AWS AMI then these _should_ be preinstalled. 
+
+~~~
+$ fastqc -h
+            FastQC - A high throughput sequence QC analysis tool
+
+SYNOPSIS
+
+        fastqc seqfile1 seqfile2 .. seqfileN
+
+    fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
+           [-c contaminant file] seqfile1 .. seqfileN
+
+DESCRIPTION
+
+    FastQC reads a set of sequence files and produces from each one a quality
+    control report consisting of a number of different modules, each one of
+    which will help to identify a different potential type of problem in your
+    data.
+
+    If no files to process are specified on the command line then the program
+    will start as an interactive graphical application.  If files are provided
+    on the command line then the program will run with no user interaction
+    required.  In this mode it is suitable for inclusion into a standardised
+    analysis pipeline.
+
+    The options for the program as as follows:
+
+    -h --help       Print this help file and exit
+
+    -v --version    Print the version of the program and exit
+
+    -o --outdir     Create all output files in the specified output directory.                                                                                    
+                    Please note that this directory must exist as the program
+                    will not create it.  If this option is not set then the
+                    output file for each sequence file is created in the same
+                    directory as the sequence file which was processed.
+
+    --casava        Files come from raw casava output. Files in the same sample
+                    group (differing only by the group number) will be analysed
+                    as a set rather than individually. Sequences with the filter
+                    flag set in the header will be excluded from the analysis.
+                    Files must have the same names given to them by casava
+                    (including being gzipped and ending with .gz) otherwise they
+                    won't be grouped together correctly.
+
+    --nano          Files come from naopore sequences and are in fast5 format. In
+                    this mode you can pass in directories to process and the program
+                    will take in all fast5 files within those directories and produce
+                    a single output file from the sequences found in all files.
+
+    --nofilter      If running with --casava then don't remove read flagged by
+                    casava as poor quality when performing the QC analysis.
+
+    --extract       If set then the zipped output file will be uncompressed in
+                    the same directory after it has been created.  By default
+                    this option will be set if fastqc is run in non-interactive
+                    mode.
+
+    -j --java       Provides the full path to the java binary you want to use to
+                    launch fastqc. If not supplied then java is assumed to be in
+                    your path.
+
+    --noextract     Do not uncompress the output file after creating it.  You
+                    should set this option if you do not wish to uncompress
+                    the output when running in non-interactive mode.
+
+    --nogroup       Disable grouping of bases for reads >50bp. All reports will
+                    show data for every base in the read.  WARNING: Using this
+                    option will cause fastqc to crash and burn if you use it on
+                    really long reads, and your plots may end up a ridiculous size.
+                    You have been warned!
+
+    -f --format     Bypasses the normal sequence file format detection and
+                    forces the program to use the specified format.  Valid
+                    formats are bam,sam,bam_mapped,sam_mapped and fastq
+
+    -t --threads    Specifies the number of files which can be processed
+                    simultaneously.  Each thread will be allocated 250MB of
+                    memory so you shouldn't run more threads than your
+                    available memory will cope with, and not more than
+                    6 threads on a 32 bit machine
+
+    -c              Specifies a non-default file which contains the list of
+    --contaminants  contaminants to screen overrepresented sequences against.
+                    The file must contain sets of named contaminants in the
+                    form name[tab]sequence.  Lines prefixed with a hash will
+                    be ignored.
+
+    -a              Specifies a non-default file which contains the list of
+    --adapters      adapter sequences which will be explicity searched against
+                    the library. The file must contain sets of named adapters
+                    in the form name[tab]sequence.  Lines prefixed with a hash
+                    will be ignored.
+
+    -l              Specifies a non-default file which contains a set of criteria
+    --limits        which will be used to determine the warn/error limits for the
+                    various modules.  This file can also be used to selectively
+                    remove some modules from the output all together.  The format
+                    needs to mirror the default limits.txt file found in the
+                    Configuration folder.
+
+   -k --kmers       Specifies the length of Kmer to look for in the Kmer content
+                    module. Specified Kmer length must be between 2 and 10. Default
+                    length is 7 if not specified.
+
+   -q --quiet       Supress all progress messages on stdout and only report errors.
+
+   -d --dir         Selects a directory to be used for temporary files written when
+                    generating report images. Defaults to system temp directory if
+                    not specified.
+
+BUGS
+
+    Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk
+    or in www.bioinformatics.babraham.ac.uk/bugzilla/
+~~~
+{: .bash}
+
+if fastqc is not installed then you would expect to see an error like
+
+~~~
+$ fastqc -h 
+The program 'fastqc' is currently not installed. You can install it by typing:
+sudo apt-get install fastqc
+~~~
+
+If this happens check with your instructor before trying to install it. 
 
 ## Assessing Quality using FastQC
 In real life, you won't be assessing the quality of your reads by visually inspecting your