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:[email protected]] Sent: Friday, November 05, 2010 9:28 AM To: Kunbin Qu Cc: '[email protected]' 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 >> > > > > ______________________________________________________________________ > > The contents of this electronic message, including any attachments, are intended only for the use of the individual or entity to which they are addressed and may contain confidential information. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this message or any attachment is strictly prohibited. If you have received this transmission in error, please send an e-mail to [email protected] and delete this message, along with any attachments, from your computer. > [[alternative HTML version deleted]] > > _______________________________________________ Bioc-sig-sequencing > mailing list [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 ______________________________________________________________________ The contents of this electronic message, including any attachments, are intended only for the use of the individual or entity to which they are addressed and may contain confidential information. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this message or any attachment is strictly prohibited. If you have received this transmission in error, please send an e-mail to [email protected] and delete this message, along with any attachments, from your computer. _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
