Dear users, I read through UCSC wiggle format (BigWig) in depth. I understand the format about variable step, fixed step and use of bigwig to visualize in a browser etc. However, I don't have clarity on using ChIP-Seq, ATAC-Seq data in bigWig format.
Example of the Wig file after converting from bigwig format using bigWigToWig. This example data is from ATAC-Seq.
#bedGraph section chr1:0-870999 chr1 0 9999 0 chr1 9999 10099 16.561 chr1 10099 10199 24.2045 chr1 10199 10299 2.54784 chr1 10299 10399 5.09568 chr1 10399 10499 11.4653 chr1 10499 10599 7.64352 chr1 10599 10699 3.82176 chr1 10699 13199 0
In this context, could someone help understanding: 1. What is the real number value in 4th column. Is the read depth for that position? or some transformed value of read depth. Typically in ChIP-Seq or ATAC-Seq, what is the value that one would represent in this column.
If this is threshold, how users specify thresholds for selecting significantly enriched regions. (I am not sure if any statistical test is associated with significance, I cannot find any reference but users call it so).
I have 6 ATAC-Seq bigwig files for 6 different samples. How do I find the regions of interest in at least 4 of samples.
Thank you for your help.