[Bioc-sig-seq] readAligned for Illumina's export file
Kunbin Qu
KQu at genomichealth.com
Fri Nov 5 17:54:02 CET 2010
Martin, thanks for the help. You are correct, readAligned can read those reads in when the filter is not there. The chromosome filter I had in my command did the screening which eliminated the reads mapped across the junctions, including those were on the desired chromosome (in my original bigger file), since the "chromosome" field are all "splice_sites-auto.fa". Does ShortRead have a parser to extract the splice junction coordinates from the 2nd entry in my previous email, or I need to write myself, as from the pure readAligned (ie, without "filter") it does not seem to be able to interpret the coordinates correctly. Thanks again.
-Kunbin
-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
Sent: Friday, November 05, 2010 9:28 AM
To: Kunbin Qu
Cc: 'Bioc-sig-sequencing at r-project.org'
Subject: Re: [Bioc-sig-seq] readAligned for Illumina's export file
On 11/05/2010 08:51 AM, Kunbin Qu wrote:
> Dear all,
>
> can readAligned() or other function read in the reads mapped across
> the junctions in the "export" file (eg, s_1_export.txt) from
> Illumina's pipeline? The following is the example of a regular
> mapping entry and a read mapped across two exons. I had a test file
> named s1Test, and when I used the following command, it can only read
> in the first read. Thanks.
It's tricky to know what your file looks like, but this should be parsed
by readAligned.
> x = readAligned("/tmp/kunbin_export.txt", type="SolexaExport")
> x
class: AlignedRead
length: 2 reads; width: 51 cycles
chromosome: chrX.fa
splice_sites-auto.faDHRS7_50_50_chr14.fa_59681484_59685824
position: 108773654 20
strand: + -
alignQuality: NumericQuality
alignData varLabels: run lane ... filtering contig
> sread(x)
A DNAStringSet instance of length 2
width seq
[1] 51 NTTTTAAAAACAGAATTTCTGCTCTATAATAACACAGCTAAAGGGAAATAA
[2] 51 NGAACTTTAAGAGTGGTGTGGATGCAGACTCTTCTTATTTTAAAATCTTTA
> quality(x)
class: SFastqQuality
quality:
A BStringSet instance of length 2
width seq
[1] 51 BKOJHRQPPO_QQ_____b_b___b_bb_bb__bb__b_b___bbb_b__Q
[2] 51 BKIKKUUTTU_____[[[[[[[[[[_b_____b______QQQ__b___b__
maybe your 'cfilt' filters out 'chromosomes' (which should probably have
been something else, rseq?)
> chromosome(x)
[1] chrX.fa
[2] splice_sites-auto.faDHRS7_50_50_chr14.fa_59681484_59685824
2 Levels: chrX.fa ...
More hints on what 'it can only read the first read' means might help.
Martin
>
> -Kunbin
>
> SEQUENCER01 10 1 1 5110 943 0 1
> NTTTTAAAAACAGAATTTCTGCTCTATAATAACACAGCTAAAGGGAAATAA
> BKOJHRQPPO_QQ_____b_b___b_bb_bb__bb__b_b___bbb_b__Q chrX.fa
> 108773654 F T50 199
> Y
>
> SEQUENCER01 10 1 1 2815 941 0 1
> NGAACTTTAAGAGTGGTGTGGATGCAGACTCTTCTTATTTTAAAATCTTTA
> BKIKKUUTTU_____[[[[[[[[[[_b_____b______QQQ__b___b__
> splice_sites-auto.faDHRS7_50_50_chr14.fa_59681484_59685824 20
> R A50 200 Y
>
>
>
>
>> s1t<-readAligned("./", pattern="s1Test", type="SolexaExport",
>> filter=cfil) sessionInfo()
> R version 2.11.0 (2010-04-22) x86_64-unknown-linux-gnu
>
> locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3]
> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C
> LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9]
> LC_ADDRESS=C LC_TELEPHONE=C [11]
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages: [1] stats graphics grDevices utils
> datasets methods base
>
> other attached packages: [1] ShortRead_1.6.2 Rsamtools_1.0.1
> lattice_0.19-11 [4] Biostrings_2.16.7 GenomicRanges_1.0.1
> IRanges_1.6.8
>
> loaded via a namespace (and not attached): [1] Biobase_2.8.0
> grid_2.11.0 hwriter_1.2 tools_2.11.0
>>
>
>
>
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