We're interested in testing out Trans-ABySS and comparing it with our other methods for RNA-Seq analysis. It seems to have a lot of potential for metatranscriptomics, since we may not always have a metagenome.
I've finally gotten ABySS compiled (our environment was more locked down in compiler and MPI versions than I would have liked, and made it more difficult) and I am running a test right now. I think I have all the scripts and support tools for trans-ABySS installed, but there's a chance I missed one.
Trans-ABySS expects a directory structure with results from ABySS runs with different sizes of k. Is there a script packaged with ABySS or Trans-ABySS that generates all those runs? That will make my life a lot easier than running ABySS manually, and I didn't see that in the documentation. I've got ABySS 1.2.4 and trans-ABySS 1.0, FWIW.
I'll post my continued experience with these programs here, in case anyone else looks into going down this road.
I've finally gotten ABySS compiled (our environment was more locked down in compiler and MPI versions than I would have liked, and made it more difficult) and I am running a test right now. I think I have all the scripts and support tools for trans-ABySS installed, but there's a chance I missed one.
Trans-ABySS expects a directory structure with results from ABySS runs with different sizes of k. Is there a script packaged with ABySS or Trans-ABySS that generates all those runs? That will make my life a lot easier than running ABySS manually, and I didn't see that in the documentation. I've got ABySS 1.2.4 and trans-ABySS 1.0, FWIW.
I'll post my continued experience with these programs here, in case anyone else looks into going down this road.
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