Closed Leytoncito closed 2 years ago
I was checking and running digIS, well I can use a genbank file from prokka as input. Then I checked prokka's ggf3 and it is different from the one produced by digIS, but I think somehow I will be able to fix this. Anyway, it would be very interesting to implement a prokka-style gff3 output (that includes the sequences).
Hi @Leytoncito. Thank you for your interest! I will try to answer your questions as best as I can right now, Please, see below:
Can you also share an example of gff3 file generated by prokka? I would like to look at it. Thank you.
Thanks for your Answers. its seems, that prokka file contains the genes sequences at the end of the file (##FASTA), at the beginning of the file, below ## gff3-version 3, there is lines "##sequence-region ", I guess it's the genes that have more than one annotation. Here a prokka ggf3 file GCA_000159135.1.zip
Hello, what do you think of the prokka gff file?. gff file allows it to be coupled to other programs
Hello janka2012 1) Basically, the gff file will only have the IS elements?. 2) can I use these gff later with roary or panaroo? 3) I can search IS on a Panaroo or rary output file, for example the pangenome.fa (it is a fasta). 4) prokka annotates the transposases (and many other things) and generates a gff file that later I group with some tool (example roary). digIS is better for this ?.
Sorry if my questions, I am very interested in this tool. Thanks in advance!