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I performed a ROARY from 100 genome. I got several file including gene_presence_absence.csv from the results. I want to know how many unique gene(unshared gene, based on blast homology, same gene (duplicate gene) may be unique if no homology is there between them) from presence absence csv file or other file. Kindly suggest me how to calculate total number of unique gene for each genome which is only present in one genome

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  • $\begingroup$ How do you define "unique genes"? Unique to what? You mean genetic sequences that code for protein which are only present once in a given genome? Do you mean unique to that species? Unique how? In terms of sequence? In terms of function? How much similarity do you allow? What species are you working with? Please edit your question and explain what you need and also what kind of data you have more clearly. $\endgroup$
    – terdon
    Commented Mar 15, 2023 at 12:37
  • $\begingroup$ Thank you for the reply, based on presence absence gene data file, only gene found in one genome but absent in other genome is considered as unique gene, ROARY use use presence absence data based on blast homology of protein within selected protein so, at end I want to get only unique gene from the table generated by PROKKA in gene presence absence csv file. $\endgroup$
    – Umar
    Commented Mar 15, 2023 at 13:32
  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented Mar 15, 2023 at 13:43
  • $\begingroup$ Once I did ROARY, I got several files, right, there will be some shared gene, core gene , and unique gene, right, I want to know how many unshared gene (unique gene) are present in every genome. $\endgroup$
    – Umar
    Commented Mar 15, 2023 at 14:57
  • $\begingroup$ Please edit your question and provide us with an example input file and the output you would expect. $\endgroup$
    – terdon
    Commented Mar 15, 2023 at 16:16

1 Answer 1

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Did you try query_pan_genome?

Ref. https://sanger-pathogens.github.io/Roary/

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  • $\begingroup$ Your answer could be improved with additional supporting information. Please edit to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers in the help center. $\endgroup$
    – Community Bot
    Commented Sep 26, 2023 at 12:46

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