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joshuagryphon / plastid

Position-wise analysis of sequencing and genomics data
https://plastid.readthedocs.io
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Procedure for P-site estimation using stop codon peaks #5

Closed purplerainf closed 7 years ago

purplerainf commented 7 years ago

Hi,

First of all, thank you for developing such a great tool. It is easy to use and very helpful for my analysis.

I'd like to discuss my procedure for P-site estimation using stop codon peaks, not initiation peaks.

I am analyzing a ribosome profiling data, but it shows diminished initiation peaks due to poor stress response to lysis. So the P-site estimation using the initiation peaks generated noisy results.

Thus, I tried the P-site estimation using stop codon peaks. Your tutorial mentions it but suggests using another way instead of psite script. (http://plastid.readthedocs.io/en/latest/examples/p_site.html#id13)

but I think- it could be accomplished by simply, 1) run metagene generate with _--landmark stopcodon option (set R.O.I to the stop codons) 2) run psite script with the R.O.I. 3) find peaks around 16-21nt, instead of 10-15nt to 5' end (+6nt then using initiation peaks. Because the stop codon would be at immediately downstream of A-site)

I think this is an easier way and actually, I found some peaks at 16~17nt for my data. N. Ingolia's Sciences paper (Sciences 2009) also used this estimation. (See fig. 2B in the paper) http://science.sciencemag.org/content/324/5924/218.figures-only

I look forward to hearing from you whether it makes sense or not. Please correct me if I am wrong.

Thanks.

YY.

joshuagryphon commented 7 years ago

Dear YY,

Thank you for your note! I'm sorry for not getting back to you earlier- these past few weeks have included lots of travel and other work.

In any case, this procedure looks great, and, as far as usability goes, is a significant improvement upon what I currently suggest in the documentation! With your permission I'd like to include it in the documentation.

Please let me know what you think, and thank you again for writing.

Cheers, Josh

purplerainf commented 7 years ago

I am glad to hear that it makes sense. And, of course, it would be my pleasure if I can contribute to the documentation of your great tool.

Best regards, YY.

joshuagryphon commented 7 years ago

Wonderful! I'll include it in the next update. Thank you again for your suggestion!

Best, Josh