Does anyone know of a tool to convert fast5 data to fastq?
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I do not understand the the fast5/hdf format very well. Most likely such a converter is not universal? Here is one:
This certainly needs to be amended if the data are located in other "directories" of the fast5 file when using a different pipeline.Last edited by luc; 06-20-2014, 08:45 AM.
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Sorry, the mentioned script generates FASTAs. But upon replacing "fasta" with "fastq" in line 17 it will generate indeed FASTQ files.
Originally posted by luc View PostI do not understand the the fast5/hdf format very well. Most likely such a converter is not universal? Here is one:
https://gist.github.com/nickloman/3345d05e3a4642b5306c
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Originally posted by Bukowski View PostThere's a five line python script in the Metrichor docs that shows you how to do this.
Nick's script has some advantages there.
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Originally posted by luc View PostYes, but these 5 lines are not a complete script and they do not seem to work very well - this might be a problem on my side?.
Nick's script has some advantages there.
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