FAANG List Archived Post

From hu@animalgenome.org  Fri Feb 17 11:21:39 2017
From: Sylvain Foissac <sylvain.foissac@inra.fr>
To: Members of AnGenMap <angenmap@animalgenome.org>
Subject: FAANG Europe Hackathon: March 27-28, Toulouse, France
Date: Fri, 17 Feb 2017 11:21:39 -0600

Dear all,

We are glad to announce the second Hackathon of the FAANG Europe COST
Action to be held on March 27-28 in Toulouse, France.
Deadline for application: Feb 26th, 2017.
See text below and attached form.

Best regards,
s.

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FAANG Europe Hackathon March 27-28th, 2017 - Toulouse, France

Saturation analysis of bioinformatics pipelines for the functional
annotation of livestock genomes

Despite the efforts made by large-scale scientific consortia to define
standard protocols on genomics data production and analysis, experimental
recommendations and guidelines face several challenges when it comes to
non-model organisms like livestock species. Species-specific genome
properties (GC content heterogeneity, repeats, genome completion etc)
jeopardize the reliability of standardized procedures. Fundamental
parameters like sequencing depth have been deeply investigated in model
organisms but might not be straightforwardly transposed to omics studies in
farm animals. Moreover, the constant evolution of technologies and analysis
tools emphasizes the need for generic criteria and stable Quality Control
(QC) methods to assess the robustness and reliability of standard omics
analyses.

To address this need we propose to work on a subsampling-based
post-processing method that computes the impact of subsampling size on
specific informative criteria and compares the resulting saturation
profiles with predefined reference profiles.

Objectives:

 - investigate the impact of sequencing depth (# of reads) on several QC
   criteria by processing data subsamples with FAANG analysis pipelines.
 - identify relevant criteria for specific pipelines (RNA-seq, ATAC-seq,
   ChIP-seq, etc) and define standard saturation profiles to be used as
   reference.
 - implement a QC method to validate a sequencing experiment based on a
   comparison between the reference saturation profile and a subsampling
   post-process done on the data.

A dedicated bioinformatics hackathon is held on March 27th-28th 2017 in
Toulouse, France. Anyone from CA15112 participating COST countries can
apply (http://www.cost.eu/COST_Actions/ca/CA15112?parties). Candidates
should possess strong and relevant scripting skills. FAANG Europe COST
Action provides travel and accommodation support (up to 790 Euros) for
18 participants. Further costs should be covered by the participants
themselves.

The participants will be provided with the results of RNA-seq and ATAC-seq
pipelines that have been previously ran on several subsets of sequencing
data (avian and mammal species). Different QC metrics will be investigated
to define relevant saturation profiles. For instance: library complexity,
proportion of reads in coding exons, 5’-3’ gene coverage ratio for the
RNA-seq pipeline, and number of called peaks, proportion of reads in peaks,
proportion of peaks in promoters for the ATAC-seq pipeline. Other
pipelines, metrics and datasets might additionally be considered.

To apply for participation the applicants should fill out the attached
sheet (name, affiliation, brief description of scripting skills and
background) and send it to *hackathon2017listes.inra.fr* by the 26th ofFebruary, 2017.

Application form: http://www.faang.org/docs/db/0067.docx

--
Sylvain Foissac
INRA GenPhySE, ch. de Borde Rouge
31326 Castanet Tolosan, France
+33 (0)5 61 28 55 40 <+33%205%2061%2028%2055%2040>
sylvain.foissacinra.fr