Hello there
I want to find common pieces (regions) between the below coordinates in two big files?
file1: file2:
chr1:251790423-251855075 chr1:251391746-251411804
chr1:259520908-259580523 chr1:259687605-259759271
chr1:261294390-261396569 chr1:259815659-259854201
chr2:108327854-108382699 chr2:108327854-108388888
chr20:28151226-28420685 chr20:28141234-28520687
chr3:15673814-15987811 chr3:15673814-15997815
chr10:70552773-71399757 chr10:70782782-71499757
I have tried:
cat file1 file2 | sed "s/[-:]/\t/g" | bedtools sort | bedtools merge > result
But it can only merge them. I would be thankful if I could have your kind suggestions regarding to find only common regions (without extra lengths) between two files.
•
written
by
hosin •
If you use the bash shell, you can use BEDOPS bedops with process substitutions to create an efficient one-line solution:
$ bedops --intersect <(sed "s/[-:]/\t/g" file1 | sort-bed -) <(sed "s/[-:]/\t/g" file2 | sort-bed -) > answer.bed
The result will be in answer.bed.
If you use zsh (as some on Mac OS do), then the syntax for process substitutions is slightly different, but it's the same idea. (If you use Mac OS, though, your sed command would probably be a bit different.)
Bonus BEDOPS: One advantage is the ability to specify arbitrary numbers of processes, if you have more than two files:
$ bedops --intersect <(sed "s/[-:]/\t/g" file1 | sort-bed -) <(sed "s/[-:]/\t/g" file2 | sort-bed -) ... <(sed "s/[-:]/\t/g" fileN | sort-bed -) > answer.bed
You can specify as many as you like, up to your operating system's file handle limit (usually 1021, but that can be adjusted).
Thanks to send me this information. I have installed bedops as a "bin" file and run the command exactly in the bin directory and also another directory, but still I have these errors:
bedops --intersect <(sed "s/[-:]/\t/g" ourstudy | sort-bed -) <(sed "s/[-:]/\t/g" mastudy | sort-bed -) > answer.bed
bash: sort-bed: command not found... bash: sort-bed: command not found... bash: bedops: command not found...
Do you know what is the problem?
You either need to copy binaries to /usr/local/bin or add the directory containing binaries to your PATH environment variable.
See: https://bedops.readthedocs.io/en/latest/content/installation.html#linux
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