Hello Sachit, Instructions for setting up local indexes are in our wiki here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Bowtie2 is not specifically listed, but the instructions for Bowtie and Bowtie2 are nearly identical. The same indexes are used for Bowtie2 and Tophat2. When building the index, you simply replace "bowtie-build" with "bowtie2-build" in the command string and create/modify the bowtie2_index.loc file the same as you would the bowtie_index.loc file. The Tophat2 manual has some more details about getting set up here: http://tophat.cbcb.umd.edu/manual.html Next time, for questions about local installs, using just the galaxy-dev@bx.psu.edu list is best (no need to post to multiple lists). If your question has been misunderstood, please send more details to clarify. Best, Jen Galaxy team On 12/12/12 3:46 AM, Sachit Adhikari wrote:

How do I add hg16 into the build-in index?

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