Replication time value from ENCODE data

Question

[leefall2]

Hi folks

I want to get the replication time value for every 100 kb bin size in the cancer cell line.

In Encode(/University of Washington), there are seven types of data available to download: Alignments, peaks, Percentage-normalized Signal, Raw data, Summed Densities, Valleys, Wavelet-smoothed Signal.

When I was trying to get the value from the Peaks data(.bed), there were values in only few limited regions.

Now I'm trying to get it from the bam format data but I don't know how to calculate the replication time value exactly, I only have a vague concept of how to do it.

Please let me know if you have any ideas.

Thanks

Answer 1

[t.c.a.smith]

I am not sure about using the bam data or the peaks. But I have calculated replication in 100kB bins myself. To do this I took the wavelet smoothed signal values which are given per kB and calculated the mean rep time for 100kB bins across the genome with a simple python script. Maybe that approach would work for you?