Hi,
I am trying to use bedtools to generate a list of random genome intervals
# https://bedtools.readthedocs.io/en/latest/content/tools/random.html
$ bedtools random -g hg19.genome -l 5 -n 100
chr9 54133731 54133736 1 5 +
chr1 235288830 235288835 2 5 -
chr8 26744718 26744723 3 5 +
chr3 187313616 187313621 4 5 -
chr11 88996846 88996851 5 5 -
chr13 84714855 84714860 6 5 -
chr13 10759738 10759743 7 5 -
chr6 122569739 122569744 8 5 +
chr17 50884025 50884030 9 5 -
chr11 38576901 38576906 10 5 +
I noted that there are strand info in col 6 and interval may overlap if length * number > genome length
My question is:
1) Can I safely omit col 6, if I am not need strand infomation, Its also random?
2) I observe that when length * number > genome length, this command tends to output overlapping intervals, but when length * number < genome length, the command will output non-overlapping intervals first or will there be random overlaps as well.
1 answer
The more intervals you produce, the higher the odds for overlaps, that is what 2) is observing. For 1), random is random, the strand is random as well, so removing strand still gives random intervals.
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