I've mapped raw reads obtained from Nanopore Sequencing (fastq) to a reference genome (fasta) using Graphmap2. The output is a .sam file that I would like to open with IGV.
However, after creating an index for the .sam file, I've got an error message on IGV saying: "File .sam does not contain any sequence names which match the current genome".
What can I do to solve this issue?
Thank you so much for your help!