To see how to create this alias file, see Creating a Chromosome Name Alias File in the IGV User Guide. The workaround is to either rename the chromosome names in one of the files (usually the annotation file), or to create an alias file in 2-column tab-delimited format. The most common cause for this is a mismatch in the sequence (chromosome) names between the annotation file (e.g., GFF or BED) and FASTA files. Q: I imported a genome annotation file and don't see the annotations. Load the genome FASTA file or contact the igv-help forum and request that it be added to the IGV hosted genomes. The most common causes for this are the two problems noted above for loading BAM files, and attempting to compute coverage on an unsorted file. What's wrong?Ĭheck the console output for error messages.
Q: I tried to compute coverage with igvtools and nothing was created. To see how to create this alias file, see Creating a Chromosome Name Alias File in the IGV User Guide. The workaround is to create an alias file in 2-column tab-delimited format. The most common cause for this is a mismatch in chromosome names between the BAM file and the IGV genome it is being viewed against.
Q: I loaded a BAM file and don't see anything.
