fast5 is a variant of
HDF5 the native format in which raw data from Oxford Nanopore MinION are provided. You can easily extract the reads in fast5 format into a standard fastq format, using for example
Say I have aligned these reads in
fastq format to an external reference genome, resulting in a
SAM file. Say I have then taken a subset of the
SAM file, according to the bitwise flag, to include only the reads that map to the reference. With the read ID, I can then grep them out from the file containing the reads in
fastq format, generating a subset file in
fastq format containing only the IDs that have mapped to the reference.
Now my question is, can we subset reads from the
fast5 archive according to the list of mapping reads as taken from the file with reads in
fastq format? This is for educational purposes, so that we have a smaller starting archive, and the
fastq extraction takes less cpu time.