overlap is a program that computes the overlap between two sets of genomic features. More precisely it takes two gff files of genomic features as input and for each feature of the first set, says whether it is overlapped by a feature of the second set (basic mode, however more and more precise information can be retrieved).
After getting the overlap executable, type:
without any argument to get the help.
This will give you all the possible options of overlap. Basically the output will be equal to the first input file (file1) with additional information about the overlap of its features with the features of the second file (file2). There are 4 basic modes:- Mode 0 (option -m 0) is to report boolean overlap: 1 if the feature of file1 is overlapped by a feature of file2, 0 otherwise.- Mode 1 (option -m 1) is to report quantitative overlap: the number of file2 features overlapping a file1 feature. - Negative mode (option -m -1 for example) is to report the list of coordinates of file2 features overlapping a file1 feature.- Value mode (option -m n where n>=10 and n is even) is to report the list of values located in field 10 in file2 associated to file2 features overlapping a file1 feature.
You can also ask for inclusion instead of general overlap, this is the option -i, or make a stranded overlap, this is the option -st.
Do not hesitate to contact sarahqd at gmail dot com for more information.