diff --git a/docs/content/tools/unionbedg.rst b/docs/content/tools/unionbedg.rst index 0874a6da6618dbbf5a57f71a4a5116e875afa162..e76c88677837a2de4f567461801f433f9f0f56fe 100755 --- a/docs/content/tools/unionbedg.rst +++ b/docs/content/tools/unionbedg.rst @@ -3,7 +3,7 @@ ############### *unionbedg* ############### -**unionBedGraphs** combines multiple BEDGRAPH files into a single file such that one can directly +**bedtools unionbedg** 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 @@ -13,7 +13,7 @@ Usage and option summary Usage: :: - unionBedGraphs [OPTIONS] -i FILE1 FILE2 FILE3 ... FILEn + bedtools unionbedg [OPTIONS] -i FILE1 FILE2 FILE3 ... FILEn =========================== =============================================================================================================================================================================================================== Option Description @@ -51,7 +51,7 @@ Default behavior cat sizes.txt chr1 5000 - unionBedGraphs -i 1.bg 2.bg 3.bg + bedtools unionbedg -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 @@ -68,7 +68,7 @@ Default behavior :: - unionBedGraphs -i 1.bg 2.bg 3.bg -header + bedtools unionbedg -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 @@ -87,7 +87,7 @@ Default behavior :: - unionBedGraphs -i 1.bg 2.bg 3.bg -header -names WT-1 WT-2 KO-1 + bedtools unionbedg -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 @@ -108,7 +108,7 @@ Default behavior :: - unionBedGraphs -i 1.bg 2.bg 3.bg -empty -g sizes.txt -header + bedtools unionbedg -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 @@ -131,7 +131,7 @@ Default behavior :: - unionBedGraphs -i 1.bg 2.bg 3.bg -empty -g sizes.txt -header -filler N/A + bedtools unionbedg -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 @@ -166,7 +166,7 @@ Use BEDGRAPH files with non-numeric values. chr1 0 1 A/G chr1 5 6 C/T - unionBedGraphs -i 1.snp.bg 2.snp.bg 3.snp.bg -filler -/- + bedtools unionbedg -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 -/-