Preparing genome reference in FASTA format
To prepare genome reference in FASTA format for mouse assembly NCBI37/mm9, we have two options: From UCSC Using the mm9 assembly from UCSC golden Path. Do not use the masked file chromFaMasked.tar.gz! 1# download `chromFa.tar.gz ` from UCSC golden path 2wget http://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/chromFa.tar.gz 3#or 4sync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/chromFa.tar.gz . 5 6# uncompress the downloaded file 7tar -xvzf chromFa.tar.gz 8 9# remove `*random.fa` chromosomes 10rm -rf *_random.fa 11 12# concatenate all FASTA files into a single file 13cat *....