unionbedg.rst

unionbedg

unionBedGraphs combines multiple BEDGRAPH files into a single file such that one can directly compare coverage (and other text-values such as genotypes) across multiple sample

Usage and option summary

Usage:

::

unionBedGraphs [OPTIONS] -i FILE1 FILE2 FILE3 ... FILEn

Option	Description
-header	Print a header line, consisting of chrom, start, end followed by the names of each input BEDGRAPH file.
-names	A list of names (one per file) to describe each file in -i. These names will be printed in the header line.
-empty	Report empty regions (i.e., start/end intervals w/o values in all files). Requires the '-g FILE' parameter (see below).
-g	The genome file to be used to calculate empty regions.
-filler TEXT	Use TEXT when representing intervals having no value. Default is '0', but you can use 'N/A' or any other text.
-examples	Show detailed usage examples.

Default behavior

Figure:

::

cat 1.bg chr1 1000 1500 10 chr1 2000 2100 20

cat 2.bg chr1 900 1600 60 chr1 1700 2050 50

cat 3.bg chr1 1980 2070 80 chr1 2090 2100 20

cat sizes.txt chr1 5000

unionBedGraphs -i 1.bg 2.bg 3.bg 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

-header Add a header line to the output

Figure:

::

unionBedGraphs -i 1.bg 2.bg 3.bg -header chrom start end 1 2 3 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

-names Add a header line with custom file names to the output

Figure:

::

unionBedGraphs -i 1.bg 2.bg 3.bg -header -names WT-1 WT-2 KO-1 chrom start end WT-1 WT-2 KO-1 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

-empty Include regions that have zero coverage in all BEDGRAPH files.

Figure:

::

unionBedGraphs -i 1.bg 2.bg 3.bg -empty -g sizes.txt -header chrom start end WT-1 WT-2 KO-1 chrom start end 1 2 3 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 5000 0 0 0

-filler Use a custom value for missing values.

Figure:

::

unionBedGraphs -i 1.bg 2.bg 3.bg -empty -g sizes.txt -header -filler N/A chrom start end WT-1 WT-2 KO-1 chrom start end 1 2 3 chr1 0 900 N/A N/A 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 chr1 2100 5000 N/A N/A N/A

Use BEDGRAPH files with non-numeric values.

Figure:

::

cat 1.snp.bg chr1 0 1 A/G chr1 5 6 C/T

cat 2.snp.bg chr1 0 1 C/C chr1 7 8 T/T

cat 3.snp.bg chr1 0 1 A/G chr1 5 6 C/T

unionBedGraphs -i 1.snp.bg 2.snp.bg 3.snp.bg -filler -/- chr1 0 1 A/G C/C A/G chr1 5 6 C/T -/- C/T chr1 7 8 -/- T/T -/-