Problems with loading data into IGV genome

[Julia]

I seem to be having problems with loading the following into IGV genome (eg. a pop-up message says the file does not contain any sequence names which match the current genome but I am expecting alignment and coverage, as seen in a report of the data that I am provided).  I was wondering if you could let me know what I did wrong (this is my first experience of using IGV and working with NGS data).  I tried to create a chromosome name alias file, but am also having problems with that.  Pardon me for my ignorance, but how do I go about creating an alias file in 2-column tab-delimited format?  I would be really grateful for any suggestions. 

 

Please could you also add the following genome to IGV:

GenBank Accession no AF157706 : Human herpesvirus 6B strain Z29, complete genome (162114bp)

GenBank Accession no J02459: Enterobacteria phage lambda, complete genome (48502bp)

GenBank Accession no J02400: Simian virus 40, complete genome (5243bp)

GenBank Accession no X02513: m13MP18 (7249bp)

 

Thank you .

 

 

[Jim Robinson]

Hi,

Creating the alias file is the right approach.  The error is telling you that the sequence names in your alignment file do not match those in the assembly being viewed.  If these are different assemblies, aliasing won't helpful,  but assuming they are the same sequence with different names the alias file is just a 2 column tab-delimited file with the name from the genome assembly in one column, and the corresponding name for that sequence in your bam file in the other.   You can create this in any text editor, just separate the names with a tab.

With respect to those genbank assemblies,  are ".gbk" files available?  If they are you should be able to just load them as a "Genome" file from our early access IGV.   From the (new) Genomes menu do "Load from file...",  and select your .gbk file.  Follow the early access links from the downloads page to access this version.

Jim