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?