2.7 years ago by
This utility has full fasta extraction as the default usage. If you are having problems with it or a particular .2bit file from the UCSC downloads server, I suggest contacting the UCSC Genome Browser team (http://genome.ucsc.edu/FAQ/FAQmaillist.html).
The command-usage can be obtained by just running the command without arguments or by reviewing the tool list on the UCSC downloads server under the "Source" section. I am also including it below for reference.
Take care, Jen, Galaxy team
twoBitToFa - Convert all or part of .2bit file to fasta
twoBitToFa input.2bit output.fa
-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
Sequence and range may also be specified as part of the input
file name using the syntax: