Q. Why doesn't anything work?
A. It does! But these data are not quite as easy as we'd all like. We highly recommend looking at the Galaxy help pages as they give a great intro into these types of data. Even if you are using the command line version, going through some of these videos will greatly help in understanding the files. We recommend the videos on fastq data and NGS manipulation, but there are many so look around. Galaxy help and screencasts

Q. The Galaxy implementation almost finished but stopped right before the final ReportMaker step! This is so frustrating, I was so close!
A. We know, so close and so painful! We have found that if you simple close Firefox, shutdown the virtual Linux box, and restart everything then the program will reinitialize and everything will be good.

Q. How do I use the program if I only have single-end RNA-seq reads?
A. For the command line you will simply alter the initial genome alignment to account for the single-end reads. This would be done in Tophat or other aligners. For the Galaxy implementations, we are working on a single-end read workflow from fastq. Currently, you will need to align your reads to the genome and start with the "bam" workflow.



    Adam's current SNP lists for each chromsome link
        The above lists are particularly useful for the "Command Line" method as it requires SNPs listed by chromosome.
    Download from the MEGAmapper site (a beautiful whole genome sequencing mapping tool) link
        In the Galaxy download package there are several SNP sets included.
    You can create your own SNP lists but they will have to be formatted correctly to be accepted by our scripts as currently written.

    in vivo pdf
    command line step-by-step pdf

    command line RNAmappe.R, RNAidentifie.R, RNAeffecto.R, VEPsorte.R, VCFmerge.R pdf txt license
    RNAmapper link, source code, license


For questions about the paper, the in vivo methods, or command line contact: adamcmiller at rnamapper dot org
For questions about the Galaxy implementation contact: Nikolaus_Obholzer at hms dot harvard dot edu

Adam Miller, Arish Shah, and Cecilia Moens
Division of Basic Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA

Nikolaus Obholzer and Sean Megason
Department of Systems Biology
Harvard Medical School
Boston, MA