Although the first column in the default UCSC bedgraph format has the following format "chr1 chr2 chr3 ...", we found that the the first column of wig files, converted using bedtools from Aligned.Coord.bam, could also has the no-chr-prefix format "1 2 3 ...". In the light of convenience, no-chr-prefix option is embedded and we set the default as F. New command should be: python Dapars2_Multi_Sample.py Dapars2_configure_file current_processing_chromosome (for UCSC bedgraph format), and python Dapars2_Multi_Sample.py Dapars2_configure_file current_processing_chromosome T (for no-chr-prefix format).
Although the first column in the default UCSC bedgraph format has the following format "chr1 chr2 chr3 ...", we found that the the first column of wig files, converted using bedtools from Aligned.Coord.bam, could also has the no-chr-prefix format "1 2 3 ...". In the light of convenience, no-chr-prefix option is embedded and we set the default as F. New command should be: python Dapars2_Multi_Sample.py Dapars2_configure_file current_processing_chromosome (for UCSC bedgraph format), and python Dapars2_Multi_Sample.py Dapars2_configure_file current_processing_chromosome T (for no-chr-prefix format).