Recently I've started using iGenomes (http://tophat.cbcb.umd.edu/igenomes.html) to work with Tophat-Cufflinks. I'd like to know if any of you is also using them and which is your experience. Do you still prefer downloading the annotation files from other sources and building your indexes on you own?
I'm still a newbie with iGenomes. So far the only thing I miss is some information about which is the content of the annotation genes.gtf file. Anyway, I think it's a good idea and pretty easy to use.
We also started working with iGenomes (human)....so far i would say that iGenomes is a good collection! It's much easier to work with it. Downloading all single files would be much more work. Furthermore all files have the right tags (e.g. tss_id) and right formats to guarantee a simple procedure with tophat cufflinks and co... Haven't found something bad on it yet!
The question prompted me to look at iGenomes for the first time and it looks good, useful. I think I would be inclined to merge the iGenomes info with the mass of data I already have in my custom-built tables. Having worked in genetics and with geneticists for a long time, I rather gravitate to a hybrid approach!
Absolutely. Right tags is what made me start using them. Thanks for sharing your experience!