[BioC] QuasR question
michael.stadler at fmi.ch
Mon Sep 1 10:50:09 CEST 2014
Please have a look at the documentation of qAlign. The sampleFile
argument takes the path and filename of a text file, which in turn
contains the paths and file names of the sequence or bam files.
What you do is to directly pass the bam file name, which is not the same.
QuasR comes with a few example sample files. I suggest that you copy one
of those and edit it to contain your bam files.
You can get the path to such a sample file on your system by:
On 01.09.2014 10:25, Daniel Soronellas wrote:
> 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,
> Dani Soronellas
> Chromatin & Gene Expression Lab
> Ph: 933160115 / Ext: 1115
> @: daniel.soronellas at crg.eu
> Center for Genomic Regulation, PRBB
> Av. Doctor Aiguader, 88
> 08003, Barcelona (Spain)
> De: Michael Stadler [michael.stadler at fmi.ch]
> Enviat el: dilluns, 1 / setembre / 2014 10:03
> Per a: Daniel Soronellas
> A/c: bioconductor at r-project.org
> 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.
> 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
>> Dani Soronellas
>> Chromatin & Gene Expression Lab
>> Ph: 933160115 / Ext: 1115
>> @: daniel.soronellas at crg.eu
>> Center for Genomic Regulation, PRBB
>> Av. Doctor Aiguader, 88
>> 08003, Barcelona (Spain)
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