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Command-line utilities you'll need need
- faToTwoBit from UCSC (needed if there is no 2Bit file available)
- twoBitInfo from UCSC (needed to generate the genome.txt file)
- UNIX wget (not installed by default on Mac but available on most other UNIX systems)
- UNIX sort (should be pre-installed on any UNIX system, including Mac)
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| Note |
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Once you've created the 2bit file for the genome assembly, you'll delete the .fa and the .gz files. |
Create 2bit file using faToTwoBit
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Get faToTwoBit installed:
| Code Block |
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$ wget http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/faToTwoBit $ mv faToTwoBit ~/bin $ chmod a+x ~/bin/faToTwoBit |
Convert the fa files to twoBit, using the faToTwoBit. This program (from UCSC) ; faToTwoBit will read one or more fasta files and convert them to a single 2bit file. To understand how to run it, type the name of the program. If you run it without any arguments, it will print a usage message.
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