[BioC] QuasR special case alignment

[Ugo Borello]

Thank you Michael,
The reporter genes are not part of the genome, so I am aligning my short
reads to the genome (actually chr1only in the following test) and to a fasta
file (seq.fa) containing the sequences of the two reporter genes.
But, while alignment to chr1 was relatively fast, the alignment to the fasta
file it is taking forever.
Here the code:

library(QuasR)
library(parallel)

cl <- makeCluster(4)
sampleFile <- "test.txt"
genomeName <- "chr1.fa"
auxFile <- "auxiliaries.txt"

proj1 <- qAlign(sampleFile, genome= genomeName, auxiliaryFile= auxFile,
splicedAlignment=TRUE, clObj=cl)


text.txt is formatted this way:
FileName        SampleName
31omo.fastq    Sample1


auxiliaries.txt is formatted this way:
FileName    AuxName
seq.fa          egfp
seq.fa          cre


Am I missing something here? Is there a faster way to complete my analysis?

Thank you in advance for your help

Ugo


> From: Michael Stadler <michael.stadler at fmi.ch>
> Date: Fri, 26 Apr 2013 08:40:50 +0200
> To: <bioconductor at r-project.org>
> Cc: <ugo.borello at inserm.fr>
> Subject: Re: [BioC] QuasR special case alignment
> 
> Dear Ugo,
> 
> One way to accomplish would be to put your two reporter genes into a
> fasta file, and use this as your "genome" (see ?qAlign or the vignette
> for examples of genomes in fasta format).
> 
> However, I think it would be better to align against the full genome, as
> this will avoid certain problems, such as reads being suboptimally
> aligned to your reporter genes which would align perfectly to some other
> genomic locus.
> 
> Assuming that the reporter genes are part of the genome, you could then
> count alignments using qCount() with a GRanges query containing the
> ranges of your reporter genes.
> 
> If the reporter genes are not part of the genome, you can provide your
> reporter gene sequences (as a fasta file) to qAlign, and all reads not
> aligning to the genome will be further aligned to them. The format of
> the required auxiliary file is very simple and described in section 5.2
> of the vignette.
> 
> You can open the QuasR vignette using:
> library(QuasR)
> vignette("QuasR-Overview")
> 
> Best wishes,
> Michael
> 
> On 25.04.2013 16:52, Ugo Borello wrote:
>> Good morning,
>> 
>> I am doing RNA-Seq analysis and I would like to perform an exploratory
>> analysis to first verify that 2 reporter genes are expressed in my samples.
>> 
>> Could the qAlign function perform an alignment of my short reads with two
>> reporter gene sequences, excluding the genome.
>> It seems, from my first attempt, that the 'genome' parameter is essential;
>> is this true?
>> Anyway how do I have to feed those sequences to qAlign and how do I have to
>> format my auxiliary file/files to see in the alignment statistics the number
>> of mapped reads for each reporter gene sequence separately?
>> 
>> Thank you in advance for your help.
>> 
>> Ugo
>> 
>> P.S. Let me say that QuasR is a fantastic package!
>> 
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