What it does
This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.
This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file).
Example input:
# 1.bedgraph chr1 1000 1500 10 chr1 2000 2100 20 # 2.bedgraph chr1 900 1600 60 chr1 1700 2050 50 # 3.bedgraph chr1 1980 2070 80 chr1 2090 2100 20
Examples using the Zero Coverage checkbox
Output example (without checking "Report regions with zero coverage"):
chr1 900 1000 0 60 0 chr1 1000 1500 10 60 0 chr1 1500 1600 0 60 0 chr1 1700 1980 0 50 0 chr1 1980 2000 0 50 80 chr1 2000 2050 20 50 80 chr1 2050 2070 20 0 80 chr1 2070 2090 20 0 0 chr1 2090 2100 20 0 20
Output example (with checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).:
chr1 0 900 0 0 0 (*) chr1 900 1000 0 60 0 chr1 1000 1500 10 60 0 chr1 1500 1600 0 60 0 chr1 1600 1700 0 0 0 (*) chr1 1700 1980 0 50 0 chr1 1980 2000 0 50 80 chr1 2000 2050 20 50 80 chr1 2050 2070 20 0 80 chr1 2070 2090 20 0 0 chr1 2090 2100 20 0 20 chr1 2100 247249719 0 0 0 (*)
Examples adjusting the "Filler value" for no-covered intervals
The default value is '0', but you can use any other value.
Output example with filler = N/A:
chr1 900 1000 N/A 60 N/A chr1 1000 1500 10 60 N/A chr1 1500 1600 N/A 60 N/A chr1 1600 1700 N/A N/A N/A chr1 1700 1980 N/A 50 N/A chr1 1980 2000 N/A 50 80 chr1 2000 2050 20 50 80 chr1 2050 2070 20 N/A 80 chr1 2070 2090 20 N/A N/A chr1 2090 2100 20 N/A 20
Examples using the "sample name" labels:
chrom start end WT-1 WT-2 KO-1 chr1 900 1000 N/A 60 N/A chr1 1000 1500 10 60 N/A chr1 1500 1600 N/A 60 N/A chr1 1600 1700 N/A N/A N/A chr1 1700 1980 N/A 50 N/A chr1 1980 2000 N/A 50 80 chr1 2000 2050 20 50 80 chr1 2050 2070 20 N/A 80 chr1 2070 2090 20 N/A N/A chr1 2090 2100 20 N/A 20
Non-numeric values
The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value.
Input Example:
File-1 File-2 chr1 200 300 Sample1 chr1 100 240 0.75 chr1 400 450 Sample1 chr1 250 700 0.43 chr1 530 600 Sample2
Output Example:
chr1 100 200 0 0.75 chr1 200 240 Sample1 0.75 chr1 240 250 Sample1 0 chr1 250 300 Sample1 0.43 chr1 300 400 0 0.43 chr1 400 450 Sample1 0.43 chr1 450 530 0 0.43 chr1 530 600 Sample2 0.43 chr1 600 700 0 0.43
This tool is part of the bedtools package from the Quinlan laboratory.
Citation
If you use this tool in Galaxy, please cite:
Bjoern A. Gruening (2014), Galaxy wrapper