Question: ShortRead Error message: invalid character '
0
gravatar for lauren.fitch
5 weeks ago by
lauren.fitch0 wrote:

Hi, I am trying to read a series of FASTQ files into R with the ShortRead package. It reads the first four files fine but gives an error on the fifth:

> test <- readFastq(buddy.file.list[[5]])
Error: Input/Output
  file(s):
    /sbgenomics/project-files/_5_buddy_0001.fastq
  message: invalid character '

Is the invalid character the single quote? Or is it not specified in the error message? There are single quotes in all of my files, but this is the only one that isn't being read.

shortread fastq • 47 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by lauren.fitch0
Answer: ShortRead Error message: invalid character '
0
gravatar for lauren.fitch
5 weeks ago by
lauren.fitch0 wrote:

The invalid character was a space. I was reading simulated FASTQs from PBSIM and it created some reads with spaces. Leaving this up in case it's helpful for anyone else.

ADD COMMENTlink written 5 weeks ago by lauren.fitch0
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