Question: I very much like the IGB tools and its features. While I have been able to make a good use of it, I have been facing a problem and can't seem to find a solution how much I try. I am trying to view the aligned tophat output (mapped.bam and junction files from aligned RNAseq data on the reference *A. lyrata* genome. When I load the lyrata genome on the IGB browser I can see the genome coordinate and the TAIRmRNA database (the annotated .gff file). But, after I upload a mapped.bam and junction file I am not able to see the alignment (aligned reads) with the reference and the annotation.

But, I figured that the mapped.bam and junction creates its own set of scaffold at the bottom of the default set of scaffold (one to one copy with default, but not sure why?). So, if I select a scaffold that the mapped.bam file has created I am able to see the mapped reads and the junctions but now cannot see the co-ordinate bases and the annotations. However, with A. thaliana genome there is no such problem with viewing the mapped output and junctions from RNAseq data along with genome coordinates and bases, TAIR10 mRNA database and several other databases from other labs.

Also, I see that updated version of phytozome data is available (V10.2). Is the data for A. lyrata available on IGB browser (V7) the same as V10.2?

Thanks,
Bishwa K.

Answer: Hello,

It sounds to me like the reference genome you used for the alignment step is using different names for scaffolds than the version of the sequence IGB is using.

**Some useful info**:

IGB is getting reference genome sequence and gene model annotations from a publicly accessible IGB QuickLoad site located at:

http://www.igbquickload.org/quickload

The various genomes we support are contained in folders for each genome, named for the species and the month and year of the genome assembly release.

It looks like our latest A. lyrata genome is in here:

http://www.igbquickload.org/quickload/A_lyrata_Apr_2011/

IGB uses a file called "genome.txt" to populate the list of chromosome/scaffold sequences you see in the "Current Genome" table (right side tab):

http://igbquickload.org/quickload/A_lyrata_Apr_2011/genome.txt

If you download that file and open it in Excel or a text editor, you can see all the names of the chromosomes and their sizes.

The sequence data, which IGB will load when you click the "Load Sequence" button, is in a "2bit" format file called A_lyrata_Apr_2011.2bit. We are using the "2bit" format because it's very compact and there are many utilities for working with it - mostly available from Jim Kent and the UCSC Genome Bioinformatics group. The 2bit format has some nice features that makes accessing sequence data fast and easy for IGB.

If you load a BAM file into IGB and notice that all-new sequence names are getting added to the Current Sequence table **and** when you click the "Load Sequence" button, no sequence gets loaded, then that usually means: the genome.txt and 2bit files don't contain the sequences you used to run your alignment. This could happen if your genome version is different *or* if it's the same version but is just using different names.

If using different names is the problem, then you can give IGB a list of synonyms that IGB can use to match names. So for example, if the reference genome sequence you used to do your alignments contains a sequence called "FooBar" which is the same sequence that IGB calls "foobar123", then you can tell IGB the two names mean the same thing by adding a personal synonyms "chromosomes.txt" file to IGB.

For more info about that, see: https://wiki.transvar.org/display/igbman/Personal+Synonyms

Let us know if you need any help with this.

Also, if there is a more recent version of A. lyrata genome, we'd be happy to add it to the IGB QuickLoad system - including sequence and gene model annotations.

So