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
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kirannbishwa01
If you perform the alignment yourself, it might be a good idea to actually load the fasta file together with the gtf file you used for alignment to try and visualize the mapping on the IGB. Most of the time, it might just be due to the naming problem. And just in case, you might want to read this if you want to know how to index your fasta file
This also works. To open your fasta file in IGB and use it as the reference, select File > Open Genome from File. (Or click the blue and red DNA icon in the toolbar.)
IGB will then display a window that let's you select a fasta or 2bit format file to use as the reference sequence. (Better to use 2bit - it's much faster to read :-)
You can also enter a genome version and species names. It's optional, but if you do that, then IGB will display the names you selected in the Species and Genome Version menus of the Current Genome tab. Otherwise IGB will assign a default name.
Then, click OK.
What happens at that point is that IGB will scan your reference sequence file, make a list of all the chromosomes and their sizes, and then list them in Sequence table in the Current Genome tab.
At that point, you can open your files as you would normally, including your GTF file. IGB can read GTF files produced by cufflnks.
It can also read some GFF3 files. However, GFF3 files are sometimes not read correctly because different groups interpret the GFF3 specification differently and it's hard to make sure that all GFF3 files will work with IGB. For this reason, we recommend using BED or BED-Detail to represent gene models in IGB.
If you use BED-Detail, make a regular BED file. Then add a column 13 with whatever you want the gene title to be (e.g., TP53) and add a column 14 with whatever descriptive text you'd like to see in the Selection Info tab when you click on the gene. For column 4, insert the name of the gene model, e.g., AT1G07350.1 if it's Arabidopsis. For examples, see the "bed" files on the QuickLoad site - there are many examples from many different species. The text you insert into columns 4, 13, and 14 will be available for searching under the Advanced Search tab, so it's useful to add text you think will be helpful for search, like gene name and gene function.