I am an undergraduate doing a research project comparing genes in C. elegans that have large first introns to those that have normal sized first introns. I am trying to get a random sampling of about 100-200 genes that have “normal sized” first introns and about the same number that have large first introns. Is there a way to search for genes with large first introns and genes with average sized first introns? Can this be done through WormMart, and if so, how? If not, can anyone steer me in the right direction? Any advice on how to do this would be greatly appreciated! Thank you!
I think it always needs a bit of postprocessing.
You can get the intron coordinates from the GFF and try to find the always respective first one.
Or get the exons from the GFF or WormMart and derive the intron coordinates based on them.
When you say that you want to get a sample of ‘genes’…can you be more specific about what exactly you want? Sequences? Identifiers? Both? Does it matter if the first intron is an intron of the 5’ UTR? Also, what are you defining as large and normal?