Sort BED by CDT
Sort a CDT file and its corresponding BED file by the total score in the CDT file across the specified interval
CDT File Statistics
CDT file statistics provide summary measures like mean, median, and standard deviation, along with distribution and clustering metrics, to help understand and analyze the genomic data's characteristics and variability.
Sorting Strategy
Depending on the strategy selected, the "Size of Expansion" (in bins) can mean different things.
- Sort by Center: This strategy sorts genomic BED intervals according to the scores in the CDT file at the midpoint of each BED interval.
- Sort by Index: This strategy sorts genomic BED intervals based on scores in the CDT file at a specific index position within each BED interval.
Command Line Interface
Usage:
java -jar ScriptManager.jar coordinate-manipulation sort-bed [-hV] [-c=<center>]
[-o=<outputBasename>] [-x=<index> <index>]... <bedFile> <cdtReference>
Positional Input
| Input | Description |
|---|---|
<bedFile> | the BED file to sort |
<cdtReference> | the reference CDT file to sort the input by |
Output Options
| Option | Description |
|---|---|
-o, --output=<outputBasename> | specify output file basename (no .cdt/.bed extension, script will add that) |
-z, --gzip | gzip output (default=false) |
Sort Options
These options indicate which windows to sort the files by (choose one).
| Option | Description |
|---|---|
-c, --center=<center> | sort by center on the input size of expansion in bins (default=100) |
-x, --index=<index> <index> | sort by index from the specified start to the specified stop (0-indexed and half-open interval) |
note
Note that if the value input using the -c flag is odd, it is the equivalent of using that same value minus 1.