[Bioc-sig-seq] readAligned for Illumina's export file
Martin Morgan
mtmorgan at fhcrc.org
Fri Nov 5 18:06:08 CET 2010
On 11/05/2010 09:54 AM, Kunbin Qu wrote:
> 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.
Hi Kunbin -- if you mean the info. embedded in the chromosome() entry
for the splice junction read, you'll have to write your own parser.
Other fields in the SolexaExport file are captured in
pData(alignData(aln)). Martin
>
> -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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