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danbing-tk v1.3.1 (manuscript)
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@joyeuxnoel8 joyeuxnoel8 released this 04 Mar 00:07
v1.3.1-manuscript
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Learn about vigilant mode.

This version is associated with the manuscript: "The motif composition of variable-number tandem repeats impacts gene expression"

Major changes:

  • Updated preferred usage of danbing-tk by turning on kmer filter: -kf 4 1
  • Reduces *.tr.kmers output size by saving only counts, and uses index file to reconstruct locus name and kmer names

Resources in Assets:

  • tr.good.bed: VNTR set for building RPGG

Additional resource on Zenodo:

  • VNTR statistics and annotations on 35 HGSVC assemblies
  • RPGG built from the annotations
  • GTEx gene-level eVNTR discoveries
  • GTEx gene-level eMotif discoveries
  • GTEx fine-mapping results using susieR
  • Bias matrices for HGSVC, HPRC, GTEx, and Geuvadis samples used in bias correction
  • GTEx bias-corrected kmer dosage table
  • Geuvadis bias-corrected kmer dosage table

Additional analysis scripts for bias correction, eQTL mapping, and fine-mapping are available in this repo.

Assets 3
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