Problem with IGV genome - gene track not showing up

[muka...@gmail.com]

Hi!

 

Thanks again for making the Autographa californica MNPV genome part of the IGV! I have one problem with using it however: I mapped my data using the NC_001623.1 fasta file which was thh basis for making the IGV genome I think as well. However if I then display the sorted sam-files on the IGV, it gives a load of mismatches eventhough the mapping has only allowed 2 mismatches (PPT slide #1). If I do a custom genome based on the fasta file (slide #2), the mismatches do not show up but the problem of using the custom genome is that it does not show the locations of genes (slide #3), which are nicely shown in your version. So is there a solution to this, a) can I get the fasta/gff files which you used exactly to map my data incase they are somehow different or B)  can I make the genes show up on my custom genome somehow? I tried using GFF, GFF2 and GFF3 converted from the GenBank file in http://www.ncbi.nlm.nih.gov/nuccore/NC_001623.1 and none of them shows the gene locations..

 

Thanks a lot!!

 

Best,

 

Minna

[Jim Robinson]

Hi,

If you are seeing lots of mismatches the assembly we have is not the one you aligned to,  so you should not view against it irrespective of annotations.   If you are loading GFF files and not seeing anything the problem is likely a mismatch in the contig names between your fasta and the GFF files.   These names must match, or you can create an alias file.  See the user guide for more info.

Jim

[muka...@gmail.com]

Hi again!

 

Is there a way to download the genome-files from IGV in fasta-format (or other bowtie-accepted format) so that I can map my data to the exact version which was used to create the IGV genome for AcMNPV thus avoiding any problems listed in my previous message? Thanks for your help once more!

 

Best

 

Minna

[Jim Robinson]

Hi,

There is not an automated way to do this, but in some cases there are for recently added genomes.   First you can check the source of the files on the genomes page for our user documentation and download them from there.   Alternatively,  you can follow the following procedure to find the path to the fasta file and download it via url. 

(1) open a command prompt or shell
(2) cd to the igv/genomes directory
(3) unzip the .genome file (it is a zip file).  For example
          unzip NC_016856.genome
(4) the property.txt file will have the URL to the sequence, for example
         sequenceLocation=http://igv.broadinstitute.org/genomes/seq/Salmonella_enterica_serovar_Typhimurium_14028S_uid86059/NC_016856.fna

In some cases, particularly for older genomes, the above procedure will not work as the sequences were not stored in fasta files.

Jim