Entering edit mode
8.1 years ago
Tamandua
•
0
I am trying to assign taxonomy to reads using MEGAN using the following commands.
makeblastdb -in Taxa.fasta -dbtype nucl -parse_seqids
blastn -db Taxa.fasta -query Final.fasta -max_target_seqs 1 -outfmt '6 qseqid sseqid evalue bitscore sgi sacc staxids sscinames scomnames stitle' -out results.txt
In theory, this should give me a BlastTab file readable by MEGAN. However, MEGAN does not recognise the file and crashes. Is there a problem with how I create the database or the taxonomy file?
I must preface by saying that I am extremely new to this stuff myself. I recently made a database using the makeblastdb command successfully. I notice that you did not put in "-out filename". Could this maybe be the problem? You need to specify an output file.
Try: makeblastdb -in Taxa.fasta -out TaxaDB -dbtype nucl -parse_seqids
Hope this helps, even if it is 9 weeks later!