What next gen file format can be converted to Bed format
Any format with data containing, at least, a chromosome name and a start and stop index.
If the format is text-based or can be converted into text format, you can use UNIX tools like
To save time and for reproducibility, people have written and published conversion scripts, such as
*2bed scripts in BEDOPS.
Another advantage of scripts like these is that they take care of index changes, which are easy to mess up and can otherwise cause errors in downstream analysis.
What does does it mean to sort a Bed file.
Sorting often, but not always, means lexicographical sorting on chromosome name, followed by numerical sorting on the start index, followed by numerical sorting on the stop index. This can be done efficiently with tools like BEDOPS
sort-bed or, less efficiently, with GNU coreutils
sort. Sorting is done originally for BEDOPS binaries that perform set and map operations, in order to gain significant performance and memory enhancements.