Hello Luz, To get DNA sequence your best bet would be to download the 2bit files for the relevant assembly and then use our tool twoBitToFa to extract a fasta file.
Assuming you are looking for human data you will find the 2bit file ( hg19.2bit) for download here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ If you are looking for data for another organism or assembly simply go to our downloads site: http://hgdownload.cse.ucsc.edu/downloads.html And click on the relevant "Full data set" link to be taken to the analogous directory. To read more about downloading our source code (including the twoBitToFa tool) see this help doc: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads You should find the relevant tool here: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ For any of the tools simply input the tool name at the command line to see the usage statement - i.e. for twoBitToFa: $ twoBitToFa twoBitToFa - Convert all or part of .2bit file to fasta usage: twoBitToFa input.2bit output.fa options: -seq=name - restrict this to just one sequence -start=X - start at given position in sequence (zero-based) -end=X - end at given position in sequence (non-inclusive) -seqList=file - file containing list of the desired sequence names in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189 where coordinates are half-open zero-based, i.e. [start,end) -noMask - convert sequence to all upper case -bpt=index.bpt - use bpt index instead of built in one -bed=input.bed - grab sequences specified by input.bed. Will exclude introns Sequence and range may also be specified as part of the input file name using the syntax: /path/input.2bit:name or /path/input.2bit:name or /path/input.2bit:name:start-end Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 3/22/12 4:38 PM, Orozco, Luz wrote: > Hi, is there a way to use the 'get DNA' from the unix command line? > > Luz > > IMPORTANT WARNING: This email (and any attachments) is only intended for the > use of the person or entity to which it is addressed, and may contain > information that is privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential manner. > Unauthorized redisclosure or failure to maintain confidentiality may subject > you to federal and state penalties. If you are not the intended recipient, > please immediately notify us by return email, and delete this message from > your computer. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
