ATAC and CR coverage

ATAC and C&R coverage plots for "Enhancer distance matters: forced linear recruitment of a super-enhancer strongly reactivates the developmentally silenced fetal HBG globin genes"

Figure ATAC and Cut&Run coverage

See also README methods

ATAC coverage coverage plots

• Normalisation of bigwigs: --SPMR by MACS2 ("MACS will SAVE signal per million reads for fragment pileup profiles")
• Scaling ATAC on the signal on all TSS sites (500bp up- and downstream)
• Figure specifications ATAC_coverage_figure.tsv and ATAC_coverage_figure_sup.tsv
• bigwigs: ~/Documents/projects/HbF_react/bigwigs atac/output_HbF_react_no_dedup
  • laat4 ~/source/ATAC-seq/output_HbF_react_no_dedup/bigwig
  • laat2 /storage/shared/HbF_react/ATAC-seq/output_HbF_react_no_dedup/bigwig

Cut & Run coverage plots

• Normalisation of bigwigs: deeptools bamCoverage --normalizeUsing RPGC reads per genomic content (1x normalization)

• Alignment with mapping quality 1.

• Scaling on the signal at HBA1 and HBA2

• Figure specifications CR_coverage_figure.tsv and CR_coverage_figure_sup.tsv

• bigwigs: ~/Documents/projects/VER9574/CR/low_q_mapping/

  • laat2 /storage/shared/HbF_react/Cut-and-Run/output_low_q_mapping_new/bigwig