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IMSA User Manual

IMSA User Manual

IMSA User

IMSA User Manual Created by Michelle Dimon for the Arron Lab Last edited January 10th, 2013 Installation and Configuration Unpack the tarball IMSA code is written in Python, so you must have python installed to run IMSA. It has been tested extensively on version 2.6.1 and less extensively on version 2.4.3. Any version in the 2.6 or 2.7 family should be fine, but do not use Python 3.0 as it has dramatic differences with version 2. Unpack the tarball to get the code. tar -xvf imsa.tar Make sure all dependencies are installed Depending on the types of alignments that you want to do, you will need certain programs installed and certain databases downloaded. By default, I recommend the following. Programs: bowtie blat blastn (new NCBI version) Databases (assuming human alignment): hg19 built as bowtie index hg19 built as a blat index, with associated ooc file hg19 built as a blastn index nt (blastn database from NCBI)