Entering edit mode
2.3 years ago
sciencercur
•
0
Hi! I am unable to see how I can get the bedtools cluster call to output into a file and what type of file that would be. It isn't written anywhere in the documentation. Thanks,!
The best way to answer these questions is to run
bedtools clusteryourself and see what happens. That said I was able to surmise the following from the documentation:the default output is a three column BED file with a 4th column denoting which cluster the feature has been grouped in, see https://bedtools.readthedocs.io/en/latest/content/tools/cluster.html#default-behavior for the example.
Since there is no flag for specifying the name of the output file I imagine the output is written to standard output and can be written to file by adding
> cluster_output.txtto the end of you command.thank you! that is what i did