加载中…【twoBitToFa】bed转换成fasta文件
(2014-09-19 16:29:54)
twoBitToFa程序说明:
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
-bpt=index.bpt - use bpt index instead of built
in one
-bed=input.bed - grab sequences specified by
input.bed. Will exclude introns
/path/input.2bit:name
or
/path/input.2bit:name
or
/path/input.2bit:name:start-end
twoBitToFa - Convert all or
part of .2bit file to fasta
usage:
options:
Sequence and range may also be
specified as part of the input
file name using the
syntax:
#由bed文件的位置信息，来提取相应的序列信息
twoBitToFa -bed=xxxx.bed
/leofs/noncode/reference/human/hg19/hg19.2bit out.fa
#其中,xxxx.bed为需要转换的文件，/leofs/noncode/reference/human/hg19/hg19.2bit为人类参考基因组hg19.2bit的存储路径，out.fa为输出的文件(可根据需要命名成xxx.fa)
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