[BioC] how to read empty line in the fastqfile
wang peter
wng.peter at gmail.com
Thu Mar 8 22:59:37 CET 2012
i often meet this problem after trimming the adapters
> reads <- readFastq(fastqfile);
Error: Input/Output
file(s):
L003GAF-128.trimmed
message: unexpected empty line L003GAF-128.trimmed:61
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
other attached packages:
[1] ShortRead_1.12.4 latticeExtra_0.6-19 RColorBrewer_1.0-5
[4] Rsamtools_1.6.3 lattice_0.20-0 Biostrings_2.22.0
[7] GenomicRanges_1.6.7 IRanges_1.12.6
loaded via a namespace (and not attached):
[1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.22.0 grid_2.14.1
[5] hwriter_1.3 RCurl_1.91-1 rtracklayer_1.14.4 tools_2.14.1
[9] XML_3.9-4 zlibbioc_1.0.0
--
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
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