Good Morning: Your file is a very odd combination of line control characters. It has OSX version 9 line terminators, the \r (aka CR) and it also has a single \n (aka LF) terminator. Thus, it appears as a single line to most software.
See also: http://en.wikipedia.org/wiki/Newline Such a file is going to have trouble anywhere it goes. You need to get ordinary files to work with the command line programs and with custom tracks. I don't know what is up with the software you are using, but it needs help. --Hiram ----- Original Message ----- From: "DeQuincy Prescott (UCL)" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Tuesday, February 28, 2012 4:11:18 AM Subject: Re: [Genome] Adding Chr to each line Back at work now so using a file generated on this computer $ head ptest.bed | od -c 0000000 c h r 1 7 \t 3 9 7 1 4 2 \t 3 9 7 0000020 1 5 2 \t 1 \r 1 7 \t 3 9 7 1 5 2 \t 0000040 3 9 7 1 7 1 \t 2 \r 1 7 \t 3 9 7 1 0000060 7 1 \t 3 9 7 1 8 3 \t 3 \r 1 7 \t 3 0000100 9 7 1 8 3 \t 3 9 7 1 9 2 \t 4 \r 1 0000120 7 \t 3 9 7 1 9 2 \t 3 9 7 2 0 2 \t 0000140 3 \r 1 7 \t 3 9 7 2 0 2 \t 3 9 7 2 0000160 2 1 \t 2 \r 1 7 \t 3 9 7 2 2 1 \t 3 0000200 9 7 2 3 3 \t 1 \r 1 7 \t 3 9 7 5 7 0000220 5 \t 3 9 7 6 2 7 \t 1 \r 1 7 \t 3 9 0000240 7 7 7 1 \t 3 9 7 7 9 6 \t 1 \r 1 7 0000260 \t 3 9 7 7 9 6 \t 3 9 7 8 2 0 \t 2 0000300 \r 1 7 \t 3 9 7 8 2 0 \t 3 9 7 8 2 0000320 1 \t 3 \r 1 7 \t 3 9 7 8 2 1 \t 3 9 0000340 7 8 4 1 \t 2 \r 1 7 \t 3 9 7 8 4 1 0000360 \t 3 9 7 8 4 6 \t 3 \r 1 7 \t 3 9 7 0000400 8 4 6 \t 3 9 7 8 7 0 \t 2 \r 1 7 \t 0000420 3 9 7 8 7 0 \t 3 9 7 8 9 7 \t 1 \r 0000440 1 7 \t 3 9 7 8 9 7 \t 3 9 7 8 9 8 0000460 \t 2 \r 1 7 \t 3 9 7 8 9 8 \t 3 9 7 0000500 9 4 1 \t 1 \r 1 7 \t 3 9 7 9 4 1 \t 0000520 3 9 7 9 4 2 \t 2 \r 1 7 \t 3 9 7 9 0000540 4 2 \t 3 9 7 9 4 7 \t 3 \r 1 7 \t 3 0000560 9 7 9 4 7 \t 3 9 7 9 9 1 \t 2 \r 1 0000600 7 \t 3 9 7 9 9 1 \t 3 9 7 9 9 2 \t 0000620 1 \n 0000622 I have attached the pest.bed file it has only 1 chr added on the first line. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
