The default behavior will give you after the line of A feature
The number of features in B that overlapped (by at least one base pair) the A interval
So If it is 0 (Zero) it mean it is not covered.
You could use
-d Reporting the per-base of coverage for each feature in the A file
One should use the “-d” option to create, for each interval in A, a
detailed list of coverage at each of the positions across each A
The output will consist of a line for each one-based position in each
A feature, followed by the coverage detected at that position.
and also you may want to use
-hist Creating a histogram of coverage for each feature in the A file
One should use the “-hist” option to create, for each interval in A, a
histogram of coverage of the features in B across A.
In this case, each entire feature in A will be reported, followed by
the depth of coverage, the number of bases at that depth, the size of
the feature, and the fraction covered. After all of the features in A
have been reported, a histogram summarizing the coverage among all
features in A will be reported.
for more detailed answer you should provide the command you used.
modified 17 months ago
17 months ago by
Medhat ♦ 8.2k