So I completed a BLAST run where I've matched my query 16S rRNA sequences with a custom 16S rRNA database with the following command on Unix:
/usr/local/blast/2.2.29/bin/blastn -query data/output_data/13L29Trimmed.fasta -db data/database/16sdatabaseBLAST -out output_data/13L29Blasted.blastn -evalue 1e-10 -num_threads 6 -outfmt 7 &
After completing the BLAST, I received a 1.1 GB blastn file as expected. A bioinformatics friend then told me to use MEGAN to process my BLAST results, which I did. The first thing I tried to do was to import my BLAST file into MEGAN. Even after providing MEGAN with the gi mapping file it needs to process the BLAST result, I get the following error:
Reads file(s) not given or found, RMA file will not contain read sequences
Afterwards, I find that although my reads have been successfully matched, that none of them were actually assigned.
After doing some troubleshooting, I think it's related to the output format I tried to set for my BLAST run. Reading through the manual, I found that the output option 7, the one I used, should be suitable for MEGAN processing. However, I can't get MEGAN to assign the reads.
If someone can help me see what I'm doing wrong, I'd much appreciate it!
/usr/local/blast/2.2.29/bin/blastn -query data/output_data/13L29Trimmed.fasta -db data/database/16sdatabaseBLAST -out output_data/13L29Blasted.blastn -evalue 1e-10 -num_threads 6 -outfmt 7 &
After completing the BLAST, I received a 1.1 GB blastn file as expected. A bioinformatics friend then told me to use MEGAN to process my BLAST results, which I did. The first thing I tried to do was to import my BLAST file into MEGAN. Even after providing MEGAN with the gi mapping file it needs to process the BLAST result, I get the following error:
Reads file(s) not given or found, RMA file will not contain read sequences
Afterwards, I find that although my reads have been successfully matched, that none of them were actually assigned.
After doing some troubleshooting, I think it's related to the output format I tried to set for my BLAST run. Reading through the manual, I found that the output option 7, the one I used, should be suitable for MEGAN processing. However, I can't get MEGAN to assign the reads.
If someone can help me see what I'm doing wrong, I'd much appreciate it!
