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smithlabcode / ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data
http://doi.org/djv4
GNU General Public License v3.0
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Handling read-level P-Site offsets #162

Closed mosi223 closed 1 week ago

mosi223 commented 3 weeks ago

Dear @saketkc,

I am working on assigning P-Site offsets using the tool PSite, which infers offsets for each individual read as opposed to grouping reads based on read lengths.

By default, PSite builds the offset information directly into BAM files via an additional tag, but those can be coerced into a text format if needed. Could you recommend a way to use these read-level offsets for determining translating ORFs in Ribotricer or would it require significant changes to the Ribotricer's codebase?

Thank you very much!

saketkc commented 3 weeks ago

Hi @mosi223 , thanks for your question. This is possible by specifying the --read_lengths and --psite_offsets arguments. For example, 

ribotricer detec_orfs --read_lengths 28.29,30,31 --psite_offset 10,11,12
mosi223 commented 3 weeks ago

Hi @saketkc ! Thanks for getting back so quickly! But does this not specify the offsets based on read lengths? What I would like to do is to specify offsets for each individual read, i.e., it's possible that reads of the same length will have a difference offset.

saketkc commented 1 week ago

Unfortunately this is currently not possible with ribotricer. I am also not sure I have seen a convincing argument for read level adjustment.

mosi223 commented 1 week ago

Hi @saketkc ! Thank you for the response! There's is some evidence that read-level P-site offsets increase accuracy of ORF detection. But I also understand that this is a very new development.