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.

-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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