search

filip-husnik / pseudofinder

Detection of pseudogene candidates in bacterial and archaeal genomes.
GNU General Public License v3.0
43 stars 16 forks source link

Explanation of "no_mercy" in sleuth output #61

Open zakisaati opened 12 months ago

zakisaati commented 12 months ago

Hello,

I just run the sleuth command with a pair of genomes and I found an output table for which I do not understand some column names. What is the difference between "ds" and "ds_no_mercy"? Same question for dN/dS. Which one should be consider to calculate typical dN/dS values?

Thank you very much in advance.

Arkadiy-Garber commented 11 months ago

Hi Zaki,

Thanks for your interest in Pseudofinder!

Sorry for the confusion in the output table. We plan to re-organize the output to make it more clear and concise.

Those two ds values represent alignments based on nucleotide/codons (ds) and proteins (ds_no_mercy). I recommend using the standard ds, since the nucleotide alignments are less susceptible to overestimation due to frameshifts. Same for dN/dS. Let me know if you have any additional questions!

Thanks, Arkadiy

zakisaati commented 11 months ago

Hi again,

Thank you very much! It's pretty clear now :)

Best wishes, Zaki