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Task 3a. Add illumina annotation #36

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yocra3 opened this issue Nov 10, 2020 · 2 comments · Fixed by #53
Open

Task 3a. Add illumina annotation #36

yocra3 opened this issue Nov 10, 2020 · 2 comments · Fixed by #53
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annotation Tasks for annotation team

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@yocra3
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yocra3 commented Nov 10, 2020

Add annotation from Illumina package to Epimutations. Some interesting fields to be added are:

  • Gene
  • Gene position
  • CpG Island
@yocra3 yocra3 added the annotation Tasks for annotation team label Nov 10, 2020
@yocra3 yocra3 added this to the Basic epimutations discovery milestone Nov 10, 2020
@RaqManzano RaqManzano added this to In progress in Epimutacions Nov 11, 2020
@RaqManzano RaqManzano moved this from In progress to Done in Epimutacions Nov 11, 2020
@yocra3
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yocra3 commented Nov 11, 2020

This version of the code is thought for using EPIC annotation. Should we make it compatible for 450K array?

@yocra3
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yocra3 commented Nov 11, 2020

Potential improvement: clean Illumina's gene annotation.

Each CpGs is mapped independently to all transcripts in a gene. Thus, a CpG can be annotated several times to the same gene, even to the same gene position. This can be simplified.

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