ChIP-seq data analysis course

Held in SciLifeLab Solna, from 2018-11-07 to 2018-11-09

Course Links

Pre-course material

Alternative Files Locations

• downstream analysis main tutorial

Schedule

Labs links

Part I

• ChIP-seq data processing (Main data processing workflow) [Uppmax & locally]

• ChIPQC (Alternative QC analysis) [locally]

• deepTools visualisation (Additional signal visualisations with deepTools) [Uppmax]

Part II

• Downstream analysis (Main differential binding and functional annotations workflow) [local version]

• Downstream analysis (Main differential binding and functional annotations workflow) [Uppmax version]

• ChIPseeker (ChIPseeker package for ChIP profiling, peaks annotations, visualisation and functional annotations) [local]

• Csaw (Alternative differential binding analyses) [local version]

• Broad peak calling (Calling broad peaks) [local]

• Motifs (Motifs finding) [Uppmax]

• Public resources (Finding data in public resources) [local]

• Exo-spike (Scaling normalisation for ChIP-seq with exogenous chromatin spike) [local]

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Nature submission

https://goo.gl/forms/DV48vrfqoUDBH2gq2

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Address and travel suggestions

Travel Info

Course leaders

Agata Smialowska (email: agata.smialowska@nbis.se)

Olga Dethlefsen (email: olga.dethlefsen@nbis.se)