Sequence analysis

Analyses of sequences

Requirements

Before diving into this topic, we recommend you to have a look at:

• Introduction to Galaxy Analyses

Material

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/sequence-analysis-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Editorial Board

This material is reviewed by our Editorial Board:

Yvan Le Bras

Bérénice Batut

Joachim Wolff

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Anthony Bretaudeau

Laura Leroi

Ava Hoffman

Eric Tvedte

Elizabeth Humphries

Erwan Corre

Katherine Cox

Candace Savonen

Coline Royaux

Frederick Tan

Helena Rasche

Maria Doyle

Deepti Varshney

Stéphanie Robin

Bérénice Batut

Cameron Hyde

Joachim Wolff

Natalie Kucher

Wolfgang Maier

Robert Meller

Alexandre Cormier

Funders

This material was funded by:

NHGRI GDS Community Network

Gallantries

NIH

NHGRI ANVIL

References

• SciLifeLab: QCFAIL
  Articles about common next-generation sequencing problems
• Marco-Antonio Mendoza-Parra et al: A quality control system for profiles obtained by ChIP sequencing
  Presents an approach that associates global and local QC indicators to ChIP-seq data sets as well as to a variety of enrichment-based studies by NGS.
• Ana Conesa et al: A survey of best practices for RNA-seq data analysis
  Highlights the challenges associated with each step of RNA-seq data analysis.
• Yuval Benjamini et al: Summarizing and correcting the GC content bias in high-throughput sequencing
  Summarizes the many possible sourced of GC bias for deeply sequenced samples.
• David Sims et al: Sequencing depth and coverage: key considerations in genomic analyses
  Discuss the issue of sequencing depth in the design of next-generation sequencing experiments.
• Frontiers in Genetics: Quality assessment and control of high-throughput sequencing data
  Collection of papers on quality controls for various NGS applications
• Frazer Meacham et al: Identification and correction of systematic error in high-throughput sequence data
  Reviews and proposes correction for systematic base pair errors in deep sequencing
• Guillaume Devailly et al: Heat seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
  Presents a web-tool that allows genome scale comparison of high throughput experiments
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