############### 5.8 mergeBed ############### **mergeBed** combines overlapping or "book-ended" (that is, one base pair away) features in a feature file into a single feature which spans all of the combined features. ========================================================================== 5.8.1 Usage and option summary ========================================================================== Usage: :: mergeBed [OPTIONS] -i =========================== =============================================================================================================================================================================================================== Option Description =========================== =============================================================================================================================================================================================================== **-s** Force strandedness. That is, only merge features that are the same strand. *By default, this is disabled*. **-n** Report the number of BED entries that were merged. *1 is reported if no merging occurred*. **-d** Maximum distance between features allowed for features to be merged. *Default is 0. That is, overlapping and/or book-ended features are merged*. **-nms** Report the names of the merged features separated by semicolons. =========================== =============================================================================================================================================================================================================== ========================================================================== 5.8.2 Default behavior ========================================================================== Figure: :: Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BED FILE ************* *************** ********************** ******** Result =============================== ====================== For example: :: cat A.bed chr1 100 200 chr1 180 250 chr1 250 500 chr1 501 1000 mergeBed -i A.bed chr1 100 500 chr1 501 1000 ========================================================================== 5.8.3 (-s)Enforcing "strandedness" ========================================================================== This option behaves the same as the -s option for intersectBed while scanning for features that should be merged. Only features on the same strand will be merged. See the discussion in the intersectBed section for details. ========================================================================== 5.8.4 (-n)Reporting the number of features that were merged ========================================================================== The -n option will report the number of features that were combined from the original file in order to make the newly merged feature. If a feature in the original file was not merged with any other features, a "1" is reported. For example: :: cat A.bed chr1 100 200 chr1 180 250 chr1 250 500 chr1 501 1000 mergeBed -i A.bed -n chr1 100 500 3 chr1 501 1000 1 ========================================================================== 5.8.5 (-d)Controlling how close two features must be in order to merge ========================================================================== By default, only overlapping or book-ended features are combined into a new feature. However, one can force mergeBed to combine more distant features with the -d option. For example, were one to set -d to 1000, any features that overlap or are within 1000 base pairs of one another will be combined. For example: :: cat A.bed chr1 100 200 chr1 501 1000 mergeBed -i A.bed chr1 100 200 chr1 501 1000 mergeBed -i A.bed -d 1000 chr1 100 200 1000 ========================================================================== 5.8.6 (-nms)Reporting the names of the features that were merged ========================================================================== Occasionally, one might like to know that names of the features that were merged into a new feature. The -nms option will add an extra column to the mergeBed output which lists (separated by semicolons) the names of the merged features. For example: :: cat A.bed chr1 100 200 A1 chr1 150 300 A2 chr1 250 500 A3 mergeBed -i A.bed -nms chr1 100 500 A1;A2;A3