I have fast5-files and a fastq-file from basecalling with Dorado.
When I run:
nanopolish index -d fast5_files/ reads.fastq
I get the following error:
error: could not open reads.fastq for read
As I do not have a sequencing summary file, I do not know how to do the indexing. On Github it says:
"Without this option, nanopolish index is extremely slow as it needs to read every fast5 file individually"
but not that it does not work at all. I would have gone with the "extremely slow", but now I am at a loss.
Help would be appreciated.
Thanks and best,
Matthias
Dear all,
I have fast5-files and a fastq-file from basecalling with Dorado. When I run: nanopolish index -d fast5_files/ reads.fastq I get the following error: error: could not open reads.fastq for read
As I do not have a sequencing summary file, I do not know how to do the indexing. On Github it says: "Without this option, nanopolish index is extremely slow as it needs to read every fast5 file individually"
but not that it does not work at all. I would have gone with the "extremely slow", but now I am at a loss.
Help would be appreciated. Thanks and best, Matthias