I have sequenced a bacterial genome with a MinION and I intend to assemble it with miniasm. For this, I first intend to generate the PAF file with the sequence overlaps using minimap2. In the minimap2 tool in Galaxy (I use Galaxy Europe), I understand that I have to set the configuration of the alignment parameters to the preset option “Oxford Nanopore all-vs-all overlap mapping…”, and run the tool using the same reads (my fastq file) as the reference (to build the index) and as dataset (where it says “Select a fastq dataset”). However, the tool does not allow me to provide any fastq file where it says “Select a fastq dataset”. I have verified that my file is recognized as fastq, and I have uploaded the same file twice with two different names, but it does not work. It seems that the tool does not allow to upload a fastq file in the field labeled as “Select fastq dataset”. Any clues why?
Maybe you need to use the datatype fastqsanger instead of fastq.
It looks like the tool accepts fastqsanger, fastqsanger.gz and fasta.
Just perfect! I changed the file properties to fastqsanger and worked fine. Thanks so much!