Question

how to read empty line in the fastqfile

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wang peter ★ 2.0k

@wang-peter-4647

Last seen 10.2 years ago

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 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

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ADD COMMENT • link updated 12.7 years ago by Martin Morgan 25k • written 12.7 years ago by wang peter ★ 2.0k

score 0 · Answer 1 · 2012-03-08

On 03/08/2012 01:59 PM, wang peter wrote: > 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 Reading zero-length records has been enabled in the devel version ShortRead 1.13.16; use the devel version of R and install ShortRead via source('http://bioconductor.org/biocLite.R') biocLite('ShortRead') As Steve suggests, filtering on the way out might be sensible -- fq[width(fq) != 0]. Martin > > 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 > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

score 0 · Answer 2 · 2012-03-08

Hi, On Thu, Mar 8, 2012 at 4:59 PM, wang peter <wng.peter at="" gmail.com=""> wrote: > 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 One thing you can do is to avoid having empty lines in your FASTQ file. The question is: how are they getting there? What are you using to trim your reads? If you are doing it in R then saving the output, maybe you want to subset your trimmed object and remove 0-width fastq records before saving. -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