Re: QuasR question

Dear Dr. Stadler,

Thank you for your quick answer. 
I was reviewing section 5.1 from the tutorial, specifically the sub-section:

[ Working only with BAM files after performing alignments ]

where it shows that sampleFile2 is a bam file. Then I tried my own BAM file:

genomeFile <- "genome.fa"
sampleFile2 <- "chr22.bam"
proj2 <- qAlign(sampleFile2, genomeFile)

and got the following error:

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
In addition: Warning message:
In read.table(file = file, header = header, sep = sep, quote = quote,  :
  line 1 appears to contain embedded nulls

Do you know how I can solve it?

Thank you very much for your time and support,
Sincerelly,
Dani Soronellas
Chromatin & Gene Expression Lab
Ph: 933160115 / Ext: 1115
@: [email protected]
Center for Genomic Regulation, PRBB
Av. Doctor Aiguader, 88
08003, Barcelona (Spain)
________________________________________
De: Michael Stadler [[email protected]]
Enviat el: dilluns, 1 / setembre / 2014 10:03
Per a: Daniel Soronellas
A/c: [email protected]
Tema: Re: QuasR question

Dear Dani,

I hope you don't mind me cc'ing the bioconductor list. The question may
be of interest to others.

The answer to your questions is described in the vignette (section 5.1
"Create a sample file"). Essentially, you just list the pre-existing bam
files instead of the sequence files. QuasR will then use these instead
of creating new bam files.

Let me know if that is not clear.

Best,
Michael

On 01.09.2014 09:49, Daniel Soronellas wrote:
> Dear Dr. Stadler,
>
> I contact you because I recently found the QuasR R package, which I found to be very interesting and I would like to apply in my downstream analysis for different experiments (mainly ChIP-seq).
> I have BAM files which are already mapped by a custom pipeline, and I wanted to use QuasR from this starting point. I searched on the documentation how I can load already mapped files but didn't find the answer, is it possible for you to write a few lines of code as an example of BAM file loading to the QuasR package?
>
> Thank you very much for your time and attention,
> I would really appreciate any help you can give
>
> Sincerelly,
> Dani Soronellas
> Chromatin & Gene Expression Lab
> Ph: 933160115 / Ext: 1115
> @: [email protected]
> Center for Genomic Regulation, PRBB
> Av. Doctor Aiguader, 88
> 08003, Barcelona (Spain)
>

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