syntax.md

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tutorial_hands_on	Formatting instructions

Section title

Section subtitle

Section sub sub title (absent in left menu)

This is an introduction. Examples are extracted from Galaxy exome-seq tutorial.

{% icon details %} Details (e.g. Algorithms for normalization)

Details about normalization.

Thus, normalization based on the flag has two consequences:

• first
• second

{% icon hands_on %} Hands-on within details...wow!!

1. Filter SAM or BAM, output SAM or BAM {% icon tool %}:

• {% icon param-files %} "SAM or BAM file to filter": use as input the output of the previous step
• "Filter on bitwise flag": yes
  • "Only output alignments with all of these flag bits set":
    • {% icon param-check %} "Read is mapped in a proper pair"
  • "Skip alignments with any of these flag bits set":
    • {% icon param-check %} "The read is unmapped"

{: .hands_on}

{: .details}

{% icon comment %} This is a note/comment

The Italian Society of Human Genetics (SIGU) was established on November 14, 1997, when the pre-existing Italian Association of Medical Genetics and the Italian Association of Medical Cytogenetics joined. SIGU is one of the 27 member societies of FEGS (Federation of European Genetic Societies). {: .comment}

{% icon warning %} This is a warning

Please be aware that ... {: .warning}

This is a list

1. Item 1
2. Item 2
3. Item 3
   • Sub item
     • Sub sub item

{% icon hands_on %} Hands-on: TITLE

Introduction to hands-on

1. First step

2. Second step

   {% icon comment %} This is a note

   All the files are based on hg19 reference genome {: .comment}

   {% icon warning %} This is a warning

   Please be aware that the columns to use for calculations may be different compared to the example here considered, depending on the amount of columns of your bed files. {: .warning}

   The following is a snippet (from snippets folder): {% include snippets/create_new_history.md %}

   {% icon question %} Questions

   1. Based on the report, do you think preprocessing of the reads (trimming and/or filtering) will be necessary before mapping?
   2. Which is your candidate gene?

   {% icon solution %} Solution

   1. Solution for Sequence quality is quite good overall. If anything you might consider trimming the 3' ends of reads (base qualities decline slightly towards the 3' ends) or to filter out the small fraction of reads with a mean base quality < 5.
   2. The gene was ...

   {: .solution} {: .question}

{: .hands_on}