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Please bear with me I'm a novice working with ribogalaxy mostly.
I'm trying to use someones published foot printing reads to compare to my own par-clip reads. My par-clip reads can be parsed down to a set of single coordinate points. What I'm wanting to do is map if/whether ribosomes are before or after this point - like a stall before or after.
Could someone please steer me towards the best way of doing this. The only way I've managed to get an inkling something is going on is making a transcriptome based on +/- 75bp of my clip binding sites and use genbodycovereage on that with ribosome profiling data indicating there is a bias to one site of my sites.
I'm trying to use someones published foot printing reads to compare to my own par-clip reads. My par-clip reads can be parsed down to a set of single coordinate points. What I'm wanting to do is map if/whether ribosomes are before or after this point - like a stall before or after.
Could someone please steer me towards the best way of doing this. The only way I've managed to get an inkling something is going on is making a transcriptome based on +/- 75bp of my clip binding sites and use genbodycovereage on that with ribosome profiling data indicating there is a bias to one site of my sites.