IGV sequence name error .sam file

Question

[A_heath]

Hi all,

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!

Answer 1

[Antonio R. Franco]

To use IGV you need to upload the file containing the fasta file containing the genome, its corresponding GFF containing the gene's name and features, and the sam file including its index

If you load an unrelated GFF genome file that does not include the same gene names that the one used to generate the SAM file, the process fail