How to create a file with annotation track distribution over 1mb bin across a genome

Question

[dabitz66]

Dear all,

I have several annotation track files in bed format and want to convert them in files which give the information about the distribution density in 1mb or 5mb bins across a genome. For instance, I want to check the distribution density of transposable elements versus genic sequences and so on. What is the best tool or way to create such files that could them be used to create plots with Circos.

Thank you! André

Answer 1

[Jorge Amigo]

There's no online documentation for that module, but bedtools makewindows seems to be what you're looking for.

From bedtools makewindows command line help:

Tool: bedtools makewindows
Version: v2.29.2
Summary: Makes adjacent or sliding windows across a genome or BED file.
Usage: bedtools makewindows [OPTIONS] [-g <genome> OR -b <bed>]  [ -w <window_size> OR -n <number of windows> ]

[dabitz66]

Thanks! But how can I have a column with the calculation of the distribution density? This seems to break nicely into the desired windows but does not gives information about the distribution density, like in a bedgraph file...

[Jorge Amigo]

If you have the windows generated, you have to calculate that desired distribution on them. Maybe using bedtools intersect?