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mtisza1 / Cenote-Taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
MIT License
54 stars 7 forks source link

About output files #16

Closed xxxkkkmmm closed 2 years ago

xxxkkkmmm commented 3 years ago

Hello, Mike! First of all, thank you very much for providing us with such a good tool, but I think this tool is not very friendly to noob (such as me). I am a first-year post-graduate student and just started studying bioinformatics. I used CT2 to analyze some virus sequences, but the output files stumped me. Many of them are file types I haven't seen before and I don't know how to open them. Except for .gbf files, I can use any genome/plasmid viewer to open them, but what tools should I use to open and view other files? Hope to get your answers and help, thank you very much!

out1 out2
mtisza1 commented 3 years ago

Hi!

Thanks for trying Cenote-Taker 2, and I'm glad you were able to open the .gbf file.

All of the other files can be opened in any text editor. I like Sublime Text, but there are many options. You can also open any .csv or .tsv file in Microsoft Excel for better viewing/sorting (e.g. the "_CONTIG_SUMMARY.tsv" file).

The .sqn files can be opened in a text editor, but they are not really human readable, and are what you would use to deposit sequences in GenBank, if you added proper metadata and want to deposit them.

Let me know if you have any other issues.

Mike

xxxkkkmmm commented 3 years ago

Thank you very much for your answers! There are no more questions for now.