Bowtie2 & Tophat2 (from binary)
Fast and sensitive read alignment
wget http://garr.dl.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-linux-x86_64.zip unzip bowtie2-2.1.0-linux-x86_64.zip
mv bowtie2-2.1.0 /usr/local/bin/ ln -s /usr/local/bin/bowtie2-2.1.0/bowtie2 /usr/local/bin/ ln -s /usr/local/bin/bowtie2-2.1.0/bowtie2-build /usr/local/bin/ ln -s /usr/local/bin/bowtie2-2.1.0/bowtie2-inspect /usr/local/bin/ ln -s /usr/local/bin/bowtie2-2.1.0/bowtie2-align /usr/local/bin/ chown -R root:root /usr/local/bin/bowtie2-2.1.0
A spliced read mapper for RNA-Seq.
wget http://tophat.cbcb.umd.edu/downloads/tophat-2.0.13.Linux_x86_64.tar.gz tar xvfz tophat-2.0.13.Linux_x86_64.tar.gz
mv tophat-2.0.13.Linux_x86_64 /usr/local/bin/ ln -s /usr/local/bin/tophat-2.0.13.Linux_x86_64/tophat2 /usr/local/bin/ chown -R root:root /usr/local/bin/tophat-2.0.13.Linux_x86_64
wget http://tophat.cbcb.umd.edu/downloads/test_data.tar.gz tar zxvf test_data.tar.gz cd test_data/ tophat2 -r 20 test_ref reads_1.fq reads_2.fq |
rachaelx/bowtop2.txt ยท Last modified: 2015/04/29 08:42 by giancarlo
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Developers: CNR Ceris IT Office and Library
Giancarlo Birello (g.birello _@_ ceris.cnr.it) and Anna Perin (a.perin _@_ ceris.cnr.it) |
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