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Find Annotations
The utility findAnnotations
finds annotations of the regions specified in .bed file from the .gff file.
Prerequisites
1) A .bed file and a .gff file
How
to run it?
Type java -jar PAVED.jar findAnnotations -h
to see list of parameters
findAnnotations utility takes as input two parameters 1) .bed file and
2).gff file and outputs the annotations for the regions specified in .bed file
from the .gff file
Run the utility as follows:
java
-jar C:\Britta\manuscript\Analysis\PAVED.jar findAnnotations -i C:\Britta\manuscript\Analysis\data\FAIRE\normalizedData\FaireRepvsInput.peaks
-j
C:\Britta\manuscript\Analysis\data\annotations\LmajorFriedlin_TriTrypDB-4.0.gff
-o
C:\Britta\manuscript\Analysis\data\FAIRE\normalizedData\FaireRepvsInput.annot
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Here, "C:\Britta\manuscript\Analysis\" is the location where the jar file is present on the
local disk, -i is the peaks or valleys file in .bed format generated
using paved, -j is the .gff file containing annotations and -o is the
output file with annotations of regions in the .bed file if any.
Sample
output
The sample
output is as follows:
The columns in the output file are as follows:
1) Chromosome name
2), 3) Start and end positions of a region as specified in the .bed file
4), 5) Start and end positions of the annotated region from the .gff file
6) Description of this region as specified in column 9 of the .gff file
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