[Bioc-sig-seq] Package ShortRead: occurenceFilter and chromosomeFilter("NM")

[Ivan Gregoretti]

Hi Valerie.

That means that occurrenceFilter works strictly as advertised.

That is fine. Thank you.

Ivan


Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1016 and 1-301-496-1592
Fax: 1-301-496-9878



On Fri, May 13, 2011 at 5:55 PM, Valerie Obenchain <vobencha at fhcrc.org> wrote:
> Hi Ivan,
>
> How you filter depends on what type of file you have. If you have a bam
> file, you can use scanBam and ScanBamParam to subset the reads before they
> are read in.
>     p <- ScanBamParam(flag=scanBamFlag(isUnmappedQuery=TRUE,
> isDuplicate=FALSE))
>     unaligned <- scanBam(file, params=p)
>
> If you have a Solexa export file you will have to remove the aligned reads
> after you read the data in. The occurrenceFilter can be used to omit
> duplicates but not to select unaligned reads.
>     exptPath <- system.file("extdata", package = "ShortRead")
>     sp <- SolexaPath(exptPath)
>     aln <- readAligned(sp, "s_2_export.txt",
> filter=occurrenceFilter(duplicates="none"))
>
> The "NA" values end up in the chromosome slot of the AlignedRead object.
> Subset on the unaligned reads,
>     unaligned <- aln[chromosome(aln) == "NM"]
>
>
> Valerie
>
>
>
>
>
> On 05/13/2011 10:30 AM, Ivan Gregoretti wrote:
>
> Hello everyone,
>
> When loading reads with ShortRead::readAligned(), one has the great
> convenience of filtering the input.
>
> If I intend to load only unique sequences that are unaligned ("NM"),
> can I use occurenceFilter?
>
> By _unique_ I mean that if the sequence ATCTCATAGTGGG has been loaded
> once, I do not want to load it the next time it is found.
>
>
> ?srFilter clearly documents how aligned reads are occurenceFilter-ed,
> however, unaligned reads are not mentioned.
>
> Thank you,
>
> Ivan
>
>
> Ivan Gregoretti, PhD
> National Institute of Diabetes and Digestive and Kidney Diseases
> National Institutes of Health
> 5 Memorial Dr, Building 5, Room 205.
> Bethesda, MD 20892. USA.
> Phone: 1-301-496-1016 and 1-301-496-1592
> Fax: 1-301-496-9878
>
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