Hello Mehmet, To be clear, the utility comes from UCSC, it is not a part of a linux install (ubuntu or other).
Did you download the kent source and compile the twoBitToFa utility? Or ftp the compiled version from hgdownload? If so, double check that the utility is executable and in your shell path. If you need to obtain the utility, an executable version can be downloaded here via ftp: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ Ftp help: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download1 (follow instructions, except cd into the directory above) Complete source, from which you can compile the utility yourself: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download27 Please let us know if you continue to have trouble, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/11/10 6:34 PM, Mehmet Ilyas COSACAK wrote: > Hi, > > I am trying to convert "hg19.2bit" to "hg19.fa" by the "twoBitToFa". I > downloaded both files. I have "ubuntu" linux software. I used the following > command line to convert the "2bit" to "fa" format as : "twoBitToFa hg19.2bit > hg19.fa" but it says "twoBitToFa" is not recognized as a command. > > what sould I do to use "twoBitToFa" on linux. > > sincerely, > > mehmet. > _______________________________________________ Genome maillist - Genome@lists.soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
