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List:       bioconductor
Subject:    Re: [BioC] htSeqTools - filtered reads > BED?
From:       Michael Lawrence <lawrence.michael () gene ! com>
Date:       2012-01-27 13:08:06
Message-ID: CAOQ5Nycd8qVC-mFWA3OGEG9U7PMCo2TvjS36XvvVyQnoe2MoBw () mail ! gmail ! com
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Not familiar with htSeqTools, but it's probably as easy as:

*rtracklayer::export(ranges01Fil*, "filtered_reads.bed")

But I am not sure if you really want to use a BED file for the reads? It
seems we really need an ID-based filterBam function.

Michael

On Fri, Jan 27, 2012 at 3:56 AM, Ian Donaldson <
Ian.Donaldson@manchester.ac.uk> wrote:

>  I have found the htSeqTools methods useful for creating PCA plots of
> samples.  The filtering of reads to remove those that are deemed to be over
> amplified looks very interesting.
>
> The function is called like this:
> # BAM to IRanges object:
> *reads01 <- readAligned(dirPath , "reads01.bam", type='BAM')
>
> ranges01 <- RangedData(ranges=IRanges(position(**reads01**),position(**
> reads01**)+width(**reads01**)), space=chromosome(**reads01**),
> strand=strand(**reads01**))*
>
> *ranges01Fil <- filterDuplReads(ranges01, fdrOverAmp=0.01)*
>
> However, how can i get the filtered reads (ranges01Fil) out as BED
> formatted files?
>
> Thank you!
> Ian
>

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