[BioC] Illumina QC using ShortRead

[Martin Morgan]

On 10/07/2010 10:32 AM, Davide Cittaro wrote:
> Hi all, in order to produce some QC report we currently use the
> ShortRead qa pipeline, like this:
> 
> qual<-qa(PATH_TO_GERALD_DIRECTORY,
> pattern=".*export.txt",type=c("SolexaExport"))
> 
> We produce eland alignments only for this purpose and it takes so
> much time. Also, the QA process is taking more and more time as the
> throughput of Illumina machine increases... We've been trying to run
> with BAM files (which is the default for us, as we use bwa only), but
> we can't get the same report with same sections... Which is the
> fastest way to have decent QC without the Illumina pipeline?
> 
> THanks

Hi Davide --

use readAligned, type="BAM", and then do a qa report on that. Do this
separately for each file, and combine the qa objects with rbind. Here's
one version

library(ShortRead)
fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
fls <- c(fl, fl, fl)

qa <- do.call(rbind, Map(function(fl, id, ...) {
    aln <- readAligned(fl, type="BAM", ...)
    qa(aln, id)
}, fls, paste(basename(fls), seq_along(fls), sep="-")))

Consider using ScanBamParam() (from Rsamtools).

This is more directly supported in the devel version of ShortRead.

Maybe this doesn't get the same qa report sections precisely; which
information are you looking for?

Martin

> 
> 
> d
> /*
> Davide Cittaro
> 
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
> 
> tel.: +39(02)574303007
> e-mail: davide.cittaro at ifom-ieo-campus.it
> */
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793