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I just received my first nanopore data set and was sent a fastq file. I was expecting a fast5 file, and now I'm not sure how to begin filtering the data. Most of the tools I've come across (NanoOK, poretools) deal with the fast5 format, although they all offer ways to convert from fast5 to fastq, their tools only take fast5 input.

When I try to use the fastq_quality_filter I get a stack smashing error...

7tbear7
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Usually the first step in Nanopore data analysis is to convert from fast5 to fastq, so they actually saved you work. Further analysis can be done with fastq in software like poretools, Porechop or poRe. Your error in fastq_quality_filter probably has other reason.

tlask
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    Are you sure? A lot of the documentation for those programs (such as poretools) looks like they only accept fast5 as input. – 7tbear7 Aug 28 '17 at 16:47
  • Yes but the downstream analysis si done with fastq or fasta after conversion. Check [this](http://poretools.readthedocs.io/en/latest/content/examples.html#poretools-fastq). – tlask Sep 03 '17 at 13:55