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showing bacterial alignment, used viral database

Open priyatamapandey opened this issue 5 years ago • 3 comments

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. Screen Shot 2020-09-01 at 4 11 00 PM

Thank you for the help in advance, Priya

priyatamapandey avatar Sep 01 '20 23:09 priyatamapandey

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.

bbuchfink avatar Sep 02 '20 08:09 bbuchfink

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?

priyatamapandey avatar Sep 02 '20 15:09 priyatamapandey

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?

bbuchfink avatar Sep 03 '20 08:09 bbuchfink