[Bioc-sig-seq] readAligned for Illumina's export file

[Martin Morgan]

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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