twoBitToFa command line and usage - genome.soe.ucsc

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twoBitToFa – Convert all or part of .2bit file to fasta format. 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 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.--Mehmet Ilyas COSACAK Undergraduate twoBitToFa: command not found Bioinformatics. I believe you need to study a little bit more about bash and command line interfaces. The UCSC utility twoBitTofa [53] was used to obtain the. nucleotide sequences for the transcripts giving us a fastA file that was used for further compar-ative analysis. Long non-coding RNA # 之后进入twoBitToFa所在文件夹,运行如下命令: twoBitToFa input.2bit output.fa # 即 : twoBitToFa hg19.2bit hg19.fa # 就得到了hg19的fasta文件。 # 另外附上TwoBitToFa的其他参数: # options: #-seq=name - restrict this to just one sequence # - - start at given position in sequence (zero-based)

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