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  • SPP and Rsamtools Not Playing Nicely

    Hello all,

    I'm trying to analyze my ChIP-seq dataset using SPP but I keep getting the following error when I try to load my BAM files:

    "Rsamtools Bioconductor package is now required for BAM file support. Please install"

    The issue is that I have Rsamtools installed via biocLite. I can load it with no errors, and I see it in my RPackages folder. Has anyone run into a similar issue and know of a solution? I'm sure it's just a configuration problem somewhere on my end...

    Best,

    Bob

  • #2
    I'll answer my own question. When I dove into the source code a bit I found the following statement:

    if (!is.element("fastcluster", installed.packages()[, 1])) {
    stop("Rsamtools Bioconductor package is now required for BAM file support. Please install")

    I installed fastcluster (not included in the Rsamtools installation) and now it runs. Just a poorly worded warning.

    Comment


    • #3
      Thanks for taking the time to document the answer! Should help someone searching for this error down the road.

      Comment


      • #4
        Originally posted by jazz710 View Post
        I'll answer my own question. When I dove into the source code a bit I found the following statement:

        if (!is.element("fastcluster", installed.packages()[, 1])) {
        stop("Rsamtools Bioconductor package is now required for BAM file support. Please install")

        I installed fastcluster (not included in the Rsamtools installation) and now it runs. Just a poorly worded warning.
        Thank you jazz710 for sharing. I am a rookie for R coding and data analysis. I have a really naive question: How to import my RNA-Seq alignment files into R?

        My workflow: I upload my raw RNA-Seq data to the Basespace website, and used the Tophat application. After alignment, it provides the alignment files (.bam). I download it to my local Mac but I don't know how to import them to R studio with Rsamtools or other functions.

        Could you kindly tell me, please? Thank you very much.

        Comment


        • #5
          For my data this is the header for my code:

          # Load the libraries into R
          library(spp)
          library(Rsamtools)

          # ONLY NEED THIS IF YOU WANT TO RUN ANALYSES ON MULTIPLE PROCESSORS (10 in this case)
          library(snow)
          cluster <- makeCluster(10)


          data <- read.bam.tags(XYZ.bam)

          -------------------------------------------------------------------------------------------------------------------
          That worked for me! Note, to read in BAM files there a handful of prerequisite programs you need as well.

          Here's a tutorial link I followed:
          Last edited by jazz710; 03-14-2016, 08:11 AM. Reason: Added tutorial link

          Comment

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