showing bacterial alignment, used viral database

bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.

GNU General Public License v3.0

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showing bacterial alignment, used viral database #388

Open priyatamapandey opened 4 years ago

priyatamapandey commented 4 years ago

Hi, I have created viral database and when aligned my samples using Blastx only one subject is showing and it is bacteria. I have aligned more than 30 samples but only can see one subject id (WP_015983405.1). I am wondering that whether my database step is wrong? Attaching a screenshot of hit for understanding my query.

Thank you for the help in advance, Priya

bbuchfink commented 4 years ago

Are you saying that you didn't put this sequence (WP_015983405.1) into your database? Please double check your input fasta file to diamond makedb. Please also let me know your command line for diamond.

priyatamapandey commented 4 years ago

Hi, I think this sequence (WP_015983405.1) is in database. My main concern is, all the samples only matched with this sequence, there is not other hit with different sequence for all the 37 samples. Is it not unexpected?

bbuchfink commented 4 years ago

Have you tried the more sensitive modes of Diamond, like --very-sensitive? Have you tried using the online BLAST to see if there are viral hits?