Benjamin Buchfink
Benjamin Buchfink
I'll try to reproduce it but it may not be that easy.
No, you could only filter you database yourself for such sequences.
Can you check for a `nr.pal` file in that directory? If it doesn't exist, the database was probably not downloaded correctly.
The second command downloads the database in FASTA format, not as a BLAST database.
Both is fine, if you need taxonomic information you need to build the database from fasta.
Good cutoff settings depend a lot on the application, I can't really answer that without knowing more about it. Coverage means that the alignment between the representative and the cluster...
Your target sequences seem to be DNA or am I missing something?
You would have to use very short seeds (like `--shape-mask 11111`) and also change a number of internal cutoffs (see advanced options in the command line help) for this to...
This should not happen normally, I will have to try whether I can reproduce the issue.
With default settings normally all alignments within 10% of the best score are used for the LCA, maybe there are none? You can show me your command line and alignment...