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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