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
----- Original Message -----
From: "Daofeng Li"
To: "Hiram Clawson"
Cc: "Ivan Adzhubey"
Sent: Tuesday, August 9, 2011 8:27:23 PM
Subject: Re: [Genome] batch extracting sequence by coordinates
Hi Hiram,
but i didnot see any explanation of twoBitToFa supporting Bed format..where is
it?
Thanks:)
Best.
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