hi all: i used ShortRead to trim some sequences max.mismatchs <- 0.25*1:nchar(DNAString(PCR2rc)) trimmedCoords <- trimLRPatterns(Rpattern = PCR2rc, subject = sread(highQuaReads), max.Rmismatch= max.mismatchs, with.Rindels=T,ranges=T) trimmedReads <- narrow(highQuaReads, start=start(trimmedCoords), end=end(trimmedCoords)) but it appear some null lines, but it is the first time to happen in my exprience @HWI-ST132:506:D0CNUABXX:3:1101:4456:1871 1:N:0:TTCACA + @HWI-ST132:506:D0CNUABXX:3:1101:4331:1931 1:N:0:TTCACA GGTGGCTGTAGTTTAGTGGTAAGAATTCTACG + ? sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-redhat-linux-gnu (64-bit) 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C 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 > -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

On 02/28/2012 08:20 AM, wang peter wrote: > hi all: i used ShortRead to trim some sequences > > max.mismatchs<- 0.25*1:nchar(DNAString(PCR2rc)) using 1:nchar(...) can be bad, e.g., when nchar() ==> 0 > 1:0 [1] 1 0 use seq_len instead, so 0.25 * seq_len(nchar(DNAString(PCR2rc))) > trimmedCoords<- trimLRPatterns(Rpattern = PCR2rc, subject = > sread(highQuaReads), max.Rmismatch= max.mismatchs, > with.Rindels=T,ranges=T) > trimmedReads<- narrow(highQuaReads, start=start(trimmedCoords), > end=end(trimmedCoords)) > > but it appear some null lines, but it is the first time to happen in > my exprience > > > @HWI-ST132:506:D0CNUABXX:3:1101:4456:1871 1:N:0:TTCACA > > + > > @HWI-ST132:506:D0CNUABXX:3:1101:4331:1931 1:N:0:TTCACA > GGTGGCTGTAGTTTAGTGGTAAGAATTCTACG > + > ? > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-redhat-linux-gnu (64-bit) > > 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C 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 >> > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793