[BioC] how to read empty line in the fastqfile

Steve Lianoglou mailinglist.honeypot at gmail.com
Thu Mar 8 23:04:35 CET 2012


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


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

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