I have loaded a genome and a gtf file into IGV to see the intron/exon structure of a gene. Now I want to align a sequence against this gene and see which parts of the sequence are falling into introns and exons of the gene.
Which program would be best to create the alignment in way IGV can read it? Which file format would be best?
When google for IGV and alignment I always come up with bam format. I think this is not very practical to use for my aim.
I included a picture of my imagination how it should look like (the green track I draw by myself, this should be the alignment file).
I would be very happy if someone have a hint for me :)
edit: In case anyone is interested: I started to write my own viewer for this purpose: