I am a new user to R and Bioconductor, so please excuse my inexperience.
I have installed R (Ver: 3.1.3) and Biconductor (Ver: 3.0) on a Windows-7, 64-bit system, as per the instructions on the Bioconductor website.
I then followed the instructions in the workflow document: "RNA-Seq workflow: gene-level exploratory analysis and differential expression" from the website, using the sample data that was supplied with the workflow. I was able to proceed through the whole workflow and completed all the steps.
I am now trying to go through the RNA-Seq workflow again, but this time using some real life experimental data that we have generated, rather than using the sample experimental data provided with the workflow.
We have a some ".fastq" and ".fastq.gz" files. I have read the sections at the beginning of the RNA-Seq workflow document, about how to start with FASTQ files and align them to a reference genome etc., and get to a point where I would have real life data in a format similar to the sample experimental data supplied with the RNA-Seq workflow. I am having trouble understanding how to do this from the instructions in the workflow. I think I need to generate .BAM files, but I am unclear how to do this.
I would appreciate any advice on how to get get started with our FASTQ file(s) and be able to use these to work through the RNA-Seq workflow.
Our FASTQ files are generated from experiments with mice. I am also unsure as to where to find a "Mouse reference Genome" to align to. The RNA-Seq workflow sample data is aligned to a Human Reference Genome. Any help with this would also be appreciated.
NOTE: I upgraded R from Ver 3.1.3 to Ver: 3.2.0, but when I tried to install the "rnaseqGene" workflow, it said that this is not available for R Ver: 3.2.0. So I have reverted back to the older environment using R Ver: 3.1.3 and Bioconductor Ver: 3.0.
The message I got when trying to install "rnaseqGene" workflow under R Ver: 3.2.0 is shown below:
Installing package into ‘C:/Users/gmul3410/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository http://bioconductor.org/packages/3.1/workflows/src/contrib
Warning: unable to access index for repository http://bioconductor.org/packages/3.1/workflows/bin/windows/contrib/3.2
package ‘rnaseqGene’ is not available (for R version 3.2.0)
Thanks for any help,