hello, all i met this problem rm(list=ls()) library(ShortRead); fastafile="unigenes.fasta" seqs <- readFasta(fastafile); Error in .read.fasta.in.XStringSet(efp_list, nrec, skip, use.names, elementType, : reading FASTA file unigenes.fasta: cannot read line 474, line is too long R version 2.13.2 (2011-09-30) Platform: x86_64-unknown-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=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_1.10.4 Rsamtools_1.4.3 lattice_0.19-33 [4] Biostrings_2.20.4 GenomicRanges_1.4.8 IRanges_1.10.6 loaded via a namespace (and not attached): [1] Biobase_2.12.2 grid_2.13.2 hwriter_1.3 [[alternative HTML version deleted]]

Hi, On Tue, Nov 29, 2011 at 12:32 PM, wang peter <wng.peter at="" gmail.com=""> wrote: > hello, all > > i met this problem > > rm(list=ls()) > library(ShortRead); > fastafile="unigenes.fasta" > seqs <- readFasta(fastafile); > > > Error in .read.fasta.in.XStringSet(efp_list, nrec, skip, use.names, > elementType, ?: > ?reading FASTA file unigenes.fasta: cannot read line 474, line is too long How long is it? You can always try opening the file in your favorite editor and introducing a carriage return there to split the sequence into two lines, perhaps. I suspect you can use the *nix `fold` command line utility to ensure that all your lines are less than, say 100 chars long, eg from the command line: $ fold -w 100 unigenes.fasta > unigenes.fold.fasta Just make sure that none of your description lines in the fasta file (the ones that start with ">whatever") aren't longer than whatever you set `-w` to be. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact