Section title

Section subtitle

Section sub sub title (absent in left menu)

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

details Details (e.g. Algorithms for normalization)

Details about normalization.

Thus, normalization based on the flag has two consequences:

• first
• second

hands_on Hands-on within details…wow!!

1. Filter SAM or BAM, output SAM or BAM tool:
   • 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”:
     • param-check “Read is mapped in a proper pair”
   • “Skip alignments with any of these flag bits set”:
     • param-check “The read is unmapped”

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).

warning This is a warning

Please be aware that …

This is a list

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

hands_on Hands-on: TITLE

Introduction to hands-on

1. First step

2. Second step

   comment This is a note

   All the files are based on hg19 reference genome

   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.

   The following is a snippet (from snippets folder):

   tip Tip: Creating a new history

   Click the new-history icon at the top of the history panel

   If the new-history is missing:

   1. Click on the galaxy-gear icon (History options) on the top of the history panel
   2. Select the option Create New from the menu

   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?

   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 …

Citing this Tutorial

1. , 2020 Formatting instructions (Galaxy Training Materials). /clinical_genomics/syntax.html Online; accessed Thu Mar 13 2025
2. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

details BibTeX

 Copy

@misc{-,
    author = "",
    title = "Formatting instructions (Galaxy Training Materials)",
    year = "2020",
    month = "01",
    day = "13"
    url = "\url{/clinical_genomics/syntax.html}",
    note = "[Online; accessed Thu Mar 13 2025]"
}
@article{Batut_2018,
        doi = {10.1016/j.cels.2018.05.012},
        url = {https://doi.org/10.1016%2Fj.cels.2018.05.012},
        year = 2018,
        month = {jun},
        publisher = {Elsevier {BV}},
        volume = {6},
        number = {6},
        pages = {752--758.e1},
        author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{\i}}rez and Devon Ryan and Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Björn Grüning},
        title = {Community-Driven Data Analysis Training for Biology},
        journal = {Cell Systems}
}