Hi!
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?
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Maybe you need to use the datatype fastqsanger instead of fastq.
It looks like the tool accepts fastqsanger, fastqsanger.gz and fasta.
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Just perfect! I changed the file properties to fastqsanger and worked fine. Thanks so much!
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