Hi, I have been wondering the following:
there are lots of methods to sequence protein-bound RNAs nowadays such as RIP, CLIP whatever-IP .. as far as I can tell from papers doing it, people just sequence what's in the IP, and use similar approach to peak calling to say if a given transcript is targeted or isn't targeted by a given protein. This is fine, but gives you binary data i.e. whether a transcript may be a target of a protein or not.
Is it wrong, in principle, to compare the read counts mapping to transcripts in IP versus read counts in input (normal RNA seq), and infer enriched transcripts in the IP based on these numbers (like IP/input ratio per gene) ? What package can be used to provide some meaningful stats?
there are lots of methods to sequence protein-bound RNAs nowadays such as RIP, CLIP whatever-IP .. as far as I can tell from papers doing it, people just sequence what's in the IP, and use similar approach to peak calling to say if a given transcript is targeted or isn't targeted by a given protein. This is fine, but gives you binary data i.e. whether a transcript may be a target of a protein or not.
Is it wrong, in principle, to compare the read counts mapping to transcripts in IP versus read counts in input (normal RNA seq), and infer enriched transcripts in the IP based on these numbers (like IP/input ratio per gene) ? What package can be used to provide some meaningful stats?