computeMatrix bed format files

Question

[Morris_Chair]

Hello everyone, I'm getting familiar with deeptools and I want to use the computeMatrix function.

In the description it says:

File name, in BED format, containing the regions to plot. If multiple bed files are given, each one is considered a group that can be plotted separately.

what type of BED file should I use? it makes confusion to me because it says that I can load more then one ..

Thank you for help

Answer 1

[Friederike]

A BED file is a simple tab-separated text file where the first three columns contain the chromosome, start and end position of a specific region of interest. There's a snippet shown in the deepTools documentation, too.

As for the effect of supplying multiple BED files -- sometimes one wants to visualize multiple groups of regions in the same plot, e.g. "promoters" and "enhancers". If that were the case, you could supply a BED file specifying the promoters and another BED file specifying the enhancers and computeMatrix will calculate the scores for these two groups of regions. You can see the difference by comparing this example that used 1 BED file to [this example that may have been generated using multiple BED files (one for C1, C2, C3). Just give it a shot, I'm sure it'll make sense once you actually try it out.