ablab
Hi, just have a quick question, Is it possible to use isoQuant to discover and quantify fusion RNAs? Thanks!
Dear @yinyuanmtu
Unfortunately, at the moment IsoQuant has no functionality for fusion discovery. It might be implemented at some point in the future.
Best Andrey
@andrewprzh Thanks Audrey for the quick response! If IsoQuant right now can't identify fusion RNAs, does that mean these kind of RNAs spanning two neighbouring genes, either in same orientation or opposite orientation,, or sometimes, the neighbouring genomic region is not annotated at all, as shown in the 3 image, will not be classified as novel transcripts?
Thanks for your help! Yinan
HI Audrey, From the images you can see that I am talking about the longer RNAs spanning more than one gene. Thanks again!
Dear @yinyuanmtu
It's hard to predict IsoQuant behavior since I never tested it on such data. However, if the there are reads that have a single consecutive (possibly spliced) alignment spanning 2 or more genes, and there are enough of such reads, there is a high chance IsoQuant will report them as novel isoforms. So, probably, worth giving it a shot.
Best Andrey
HI Andrey, Thanks alot for your helpful information! I am now playing around with the program. It already produced some interesting results! Thanks for developing IsoQuant and making it much easier to use! While I was visiting the discussion site of Isoquant, I saw somewhere people mentioned that IsoQuant won't report any RNA isoform with intron retention. Could you explain that a little bit to me? If you have any reference, can you refer that to me? I am trying to identify tools that I can use to identify polycistronic RNAs in plants. From the IGV browser I can identify the polycistronic RNAs that span 2 or 3 gene loci, but I want to find a tool to classify and quantify them across samples. Many thanks, an have a nice holiday season! Yinan
On Fri, Dec 13, 2024 at 10:01 AM Andrey Prjibelski @.***> wrote:
Dear @yinyuanmtu https://github.com/yinyuanmtu
It's hard to predict IsoQuant behavior since I never tested it on such data. However, if the there are reads that have a single consecutive (possibly spliced) alignment spanning 2 or more genes, and there are enough of such reads, there is a high chance IsoQuant will report them as novel isoforms. So, probably, worth giving it a shot.
Best Andrey
— Reply to this email directly, view it on GitHub https://github.com/ablab/IsoQuant/issues/267#issuecomment-2541646739, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUXV274R2C6X7GZBCH5REZ32FLZEPAVCNFSM6AAAAABTMUMYQ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNBRGY2DMNZTHE . You are receiving this because you were mentioned.Message ID: @.***>
Hi @andrewprzh, One more question regarding the mechanism of isoQuant classifying the RNA reads? I keep seeing one long RNA read and one short RNA read that share 5' end, but they are clearly different isoforms since both are polyadenylated and are in different length. The isoQaunt however assign them as same transcript, It is really confusing. I am wondering whether it's possible to separate them. The image attached is just one example of such case with two long RNA reads and the rest short RNAs belonging to same transcript group based on IsoQuant: Thank you very much!
@yinyuanmtu
Sorry, I somehow missed your replies.
I saw somewhere people mentioned that IsoQuant won't report any RNA isoform with intron retention. Could you explain that a little bit to me? If you have any reference, can you refer that to me?
Theoretically, there are no specific limitation on reporting transcript with intron retention. I guess the main question is read support, there should be relatively high percentage of reads supporting this intron retention.
I am trying to identify tools that I can use to identify polycistronic RNAs in plants. From the IGV browser I can identify the polycistronic RNAs that span 2 or 3 gene loci, but I want to find a tool to classify and quantify them across samples.
At some point people asked about this, but at the moment IsoQuant may report them, but certainly not classify them.
I keep seeing one long RNA read and one short RNA read that share 5' end, but they are clearly different isoforms since both are polyadenylated and are in different length. The isoQaunt however assign them as same transcript, It is really confusing. I am wondering whether it's possible to separate them.
Again, sorry for the late reply, I would probably need some read and isoform coordinates to resolve this case.
Best Andrey