TSS enrichment

Time-stamp: <2017-10-20 11:57:34="">

Inputs

  • Final bam file: PE2SE.nodup.bam

Steps

  • Calculated by using the final bam file
  • Extended TSS to -/+2kb
  • Use metaseq package to create BamSignal class, and caclulated coverageover TSS features which stores in a (length(features)*bins) NumPy array
  • Shifted the bam file to half of the read length in the 5' direction
    • to center the reads on the TN5 cut sites
  • Reversed the promoters on the minus strand
  • Use normalization method from Greenleaf et al. 2013:
    • background average noise is to use averaged coverage of 100bps at both ends
    • enrichment = coverage / background average noise

Notes

  • Dealed with the TN5 inserts already??
    • Using final bam file as input, so not consider the TN5 shift. (Fri Oct 20 11:56:39 PDT 2017).
  • How should the profile looks like? what is the sub-peak?