How to extract FASTQ from the new MinION FAST5 format using poRe

November 23, 2015
By

A little while ago I demonstrated how to extract FASTQ from MinION FAST5 files using Rscript and the Linux command line.

In that article, I described how to extract the different FASTQ data using a parameter:

# 2D is the default
invisible(apply(array(f5files), 1, printfastq))
# template
invisible(apply(array(f5files), 1, printfastq, f5path="/Analyses/Basecall_2D_000/BaseCalled_template"))
# complement
invisible(apply(array(f5files), 1, printfastq, f5path="/Analyses/Basecall_2D_000/BaseCalled_complement"))

The f5path parameter is the address of the FASTQ data within the FAST5 file, and that’s been changed recently by nanopore.  Well, we can very easily simply edit our scripts to cope with the new format:

# 2D is the default
invisible(apply(array(f5files), 1, printfastq))
# template
invisible(apply(array(f5files), 1, printfastq, f5path="/Analyses/Basecall_1D_000/BaseCalled_template"))
# complement
invisible(apply(array(f5files), 1, printfastq, f5path="/Analyses/Basecall_1D_000/BaseCalled_complement"))

And that’s it! No new version of poRe required, simply a couple of edits to scripts – example scripts can be found on github.



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