Nowlan Freese

Hi Stephanie, You will need to load the genome sequence file from dryad (american_eel_genome_v5.fasta) as a custom genome in IGB instead of the genome sequence file from NCBI (GCA_001606085.1_ASM160608v1_genomic.fna.gz). Then load the gff file I previously attached (american_eel_genome_v5.sorted.gff.gz). I have attached a screenshot of what this looks like on my IGB. I don't know too much about the american eel genome, but the sequence and annotation on NCBI (mentioned in your Biostars post) is formatted...

Hi Stephanie, The issue appears to be with the gff file you are trying to view. The file does not appear to contain gene annotations mapped to a genome. The Anguilla rostrata (American eel) annotation is available from dryad. If you unpack the file, there is a file called american_eel_genome_v5.gff that appears to contain the annotation. I sorted and compressed the file and index (attached). Try loading it (american_eel_genome_v5.sorted.gff.gz) in IGB and let me know if it works for you. Best, N...

Hi Stephanie, The heap size at the bottom right has to do with the amount of memory (RAM) being used by IGB. By default, IGB will use 25% of your computer's available memory (but can be changed if needed). IGB manages its memory usage automatically, there's nothing you need to do. The only concern would be if you are loading lots of data at once and running out of available memory. Nothing in IGB should take many hours, retrieving chromosomes normally takes a few seconds. How much memory do you have...

Hi Stephanie, To load a custom genome, IGB is looking for sequence files such as fasta, fna, or 2bit. If the genome for your data is not available, and you do not have a sequence file, you can drag and drop the .gff file directly into IGB and then click Load Data. Let me know if that helps. Nowlan

Hi Stephanie, To load a custom genome, IGB is looking for sequence files such as fasta, fna, or 2bit. If the genome for your data is not available, and you do not have a sequence file, you can drag and drop the .gff file directly into IGB and then click Load Data. Let me know if that helps. Nowlan

Dear Nicolas, Thank you for using IGB, we are happy to hear that you are getting...

Dear Nicolas, Thank you for using IGB, we are happy to hear that you are getting...