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a modified version of FunSeq2 using new data context

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FunSeq2 with data context version 3

a modified version of data context for funseq2 at PCAWG project

Pre-built data context sources

  1. used by [ FunSeq2_DC version 3 ] (http://khuranalab.med.cornell.edu/data.html)
  2. used by FunSeq2 publication
FunSeq2 modifications:
  1. Fix new spliceOverlap annotations from VAT

  2. Map current terms to sequence ontology terms

  • splice_variant means either splice_donor or splice_receptor
  1. Change enhancer annotations to include tissue-specificity
  • code is modified to incorporate specific format.
  1. Remove hierarchy and annotate all

  2. Do not remove germline

  • MAF=1

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a modified version of FunSeq2 using new data context

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