readFastq error reading Nanopore fastq
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@kamalfartiyal84-7976
Last seen 3.7 years ago
Cancer Research UK Cambridge Institute

Hi, 

I am getting the following error with readFastq white trying to read in Nanopore fastq files:

Error: Input/Output

 file(s):

    /mnt/scratchb/bioinformatics/kishor01/projects/Nanopore/MinION/MN15691/fastq/MN15691.fastq

  message: line too long /mnt/scratchb/bioinformatics/kishor01/projects/Nanopore/MinION/MN15691/fastq/MN15691.fastq:1206477

 

It seems because of the limit on the read length (seems like 200000). Is there any workaround this error?

Thanks.

Kamal

 

shortread • 994 views
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@martin-morgan-1513
Last seen 13 days ago
United States

Thanks, I increased the maximum read length (from 200k to 2M bases) in version 1.34.1 / 1.35.1; these should be available via biocLite() tomorrow after about noon (all being well). If you're impatient and have devtools installed

vers = as.character(BiocInstaller::biocVersion())
branch = switch(
    vers,
    `3.5` = "RELEASE_3_5",
    `3.6` = "master",
    stop("R / Bioc too old, cannot update")
)
devtools::install_git("https://git.bioconductor.org/packages/ShortRead", branch=branch)
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@kamalfartiyal84-7976
Last seen 3.7 years ago
Cancer Research UK Cambridge Institute

Thanks Martin, I will wait for the update.

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