Good Morning: Can you please clarify what the program 'genomeCoverageBed' is and what it is working on ? Did the source files you used with 'genomeCoverageBed' have the 'chr' prefix on the chromosome numbers ?
You can simply change a file such as this with this sed command to place "chr" at the beginning of each line: sed -e 's/^/chr/' inputFile.bed > outputFile.bed You should be using chr instead of Chr if you are loading these tracks into the UCSC genome browser. --Hiram DeQuincy Prescott (UCL) wrote: > I managed to insert the header line however the genomeCoverageBed program > made each line without the "Chr" start > > i.e. > > 17 422997 422999 26 > 17 422999 423001 27 > 17 423001 423003 29 > 17 423003 423010 28 > 17 423010 423012 29 > 17 423012 423013 32 > 17 423013 423014 34 > > > instead of > > Chr17 422997 422999 26 > Chr17 422999 423001 27 > Chr17 423001 423003 29 > Chr17 423003 423010 28 > Chr17 423010 423012 29 > Chr17 423012 423013 32 > Chr17 423013 423014 34 > > Is there a way to get "Chr" inserted at the beginning of each line or is > there a way to get UCSC to read the file without it? > > Thanks > > ----------------------------------------------------- > DeQuincy Prescott > Sen Res Tech to Professor Bhattacharya _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
