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ATAC-Seq-resources.md

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This file contains ATAC-Seq resorces

  • For a full and comprehensive list of resources see

Introductory overviews

Overview of experimental and computational considerations for ATAC-seq analysis - good but a bit brief in places, doesn't go into alot of bioinformatic detail link

Lab protocols

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues nature methods paper:

  • dounce homogenise
  • density gradient centrifugation

Omni-chip - imporoved method - used for human brain slices, do nuclear extract https://www.nature.com/articles/nmeth.4396

Bioconductor Packages

esATAC

Wei Z, Zhang W, Fang H, Li Y, Wang X (2018). “esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis.” Bioinformatics. doi: 10.1093/bioinformatics/bty141. https://www.bioconductor.org/packages/release/bioc/html/esATAC.html

  • esATAC easy to use ATAC-seq pipeline - wraps alot of other R packages in an easy to use workflow - from what I see it tend to merge all fastqc of a partivcular replicate at the beginning and then carries them downstream
  • does not include IDR
  • uses chipseeker for annotation
  • uses enrichGO from clusterprofiler for GO enrichment
  • also uses motif matcher
  • does footprinitng and cutsite analysis
  • generates cutsites and filters nucleosome free fragments <100bp
  • uses F-seq for peakcalling

Chipseeker

  • annotate peaks
  • compare replicates
  • coverage plot over chromosomes

ATACSeqQC

Ou J, Liu H, Yu J, Kelliher MA, Castilla LH, Lawson ND, Zhu LJ (2018). “ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.” BMC Genomics, 19(1), 169. ISSN 1471-2164, doi: 10.1186/s12864-018-4559-3, https://doi.org/10.1186/s12864-018-4559-3.

Generates QC plots for ATAC-Seq samples

  • IGV snapshot function of specific regions
  • library complexity - distinct fragments versus putative sequenced fragments
  • frag size distribution & nucleosome phasing plot
  • shift reads for peakcalling and footprinting
  • coverage of promoter/coverage of transcript body
  • NFR score - ratio between cut sifnal adjacent to TSS:
  • nucleosome-free, mononucleosome, di nucleosome, trinucleosome fractions
    • uses random forest to classify fragments
      • top 10% reads <100bp = nucleosome free
      • top 10% of reads 180-247bp = mononucleosomes
      • this is the training set to classify the rest using randon forest - number of the three is 2*sqrt(len(training_set))
      • conservation score can also be inclused
  • heatmap and coverage curve for nucleosome possitions
    • average signal across all active TSSs
      • nuc free fragements enriched at TSS
      • nucleosome bound fragments at upstream and downstream of TSS -factor footprints does not take conservation into account (centipede = an alternative)
  • V plot - distance to binding sites

Blacklist

- Blacklist paper - https://www.nature.com/articles/s41598-019-45839-z

Footprinting

Basic experimental and computational atac-seq overview https://informatics.fas.harvard.edu/atac-seq-guidelines.html