Interpreting output produced by computeMatrix reference-point

Question

[ilovesuperheroes1993]

I have two chip sequencing samples. I want to visualize the reads within 1kb upstream / downstream of selected TSS, present in a bed file. I am using computeMatrix reference-point for this step. I have used the default parameters. In the output matrix file, each row represents a region in my bed file. The matrix contains 400 columns, each with certain values. Can anyone tell me exactly how these values are computed? Moreover, if I have specified a bin width of 10, shouldn't I get 200 columns (as the entire region spans 2 kb)?

Answer 1

[Devon Ryan]

The values in the columns are the values from the bins in your bigWig files. Since you have two samples, there are 400 rather than 200 columns (plus the first couple columns that give information about each region).