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Old 03-04-2016, 08:40 AM   #1
jazz710
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Default 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
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Old 03-04-2016, 08:51 AM   #2
jazz710
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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.
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Old 03-04-2016, 08:59 AM   #3
GenoMax
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Thanks for taking the time to document the answer! Should help someone searching for this error down the road.
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Old 03-14-2016, 07:49 AM   #4
reprogrammer
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Quote:
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.
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Old 03-14-2016, 08:08 AM   #5
jazz710
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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:
http://compbio.med.harvard.edu/Suppl.../tutorial.html

Last edited by jazz710; 03-14-2016 at 08:11 AM. Reason: Added tutorial link
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