Detailed Use: Smooth Coverage Tracks

In some special cases (like replication timing data), you have to perform signal smoothening, meaning instead of getting the coverage of one bin, you calculate the average coverage of the surrounding bins.

The smoothening parameter is changed with:

--smoothen <int>

where <int> is the number of bins on both sides to use for smoothening.

Replication Timing

In our analyses, we generally use three main parameters: 1) bin size set to 100bp, 2) set the operation to "log2" and 3) smoothening set to 500 bins. This tells BAMscale, to calculate the average of -500 to +500 bins for each bin (of length 100bp), meaning that one bin is the average of 10k bases (500bins * 100binsize * 2).

./BAMscale scale --bam Repli_seq_rB_0h_NT_rep1.sorted.dedup.bam \
    --bam Repli_seq_aB_48h_NT_rep1.sorted.dedup.bam \
    -t 8 \
    --operation log2 \
    --binsize 100 \
    --smoothen 500