There are two things: first, the Bowtie for Illumina and Bowtie for SOLiD wrappers use different data tables (bowtie_indexes as opposed to bowtie_indexes_color), which refer to different loc files (bowtie_indexes.loc and bowtie_indexes_color.loc, respectively). Secondly, although this won't effect display in the dropdown, the index files will also need to be different for use with SOLiD reads (the -C (upper case) needs to be used when creating indexes for use with color-space data).

In our case, the directory structure and index naming are standardized so it's easy to construct bowtie_indexes_color.loc based on bowtie_indexes.loc--we just add the cs subdirectory after the bowtie index directory in the path (the index files are named the same as base-space ones, so only their location is different).


On Feb 3, 2011, at 11:21 AM, Geoff Jentry wrote:

What type of data are you trying to add? For NGS references, see https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup . Let us know if that isn't enough info.

Ah, thanks Kelly. I had not come across this page. Following these instructions, I was able to get a genome to show up in the drop down for "Map with Bowtie for Illumina". However, the same drop down is not showing my genome in "Map with Bowtie for SOLiD". Any idea as to why these would be different?


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