The could be a couple of problems with the rRNA BLAST:
When we added the LSU database to the blast, since both have the string "silva" in them they both write to the same .blastout file, this overwrites half of the results
Note how they both go to the same output file -out input1.rRNA.silva.blastout:
The way we name this will have to be changed to distinguish LSU (23S/28S, LSU) and SSU (16S/18S, SSU) ribosomal RNA (rRNA). This will just take some intelligent use of regular expressions.
The could be a couple of problems with the rRNA BLAST: When we added the LSU database to the blast, since both have the string "silva" in them they both write to the same .blastout file, this overwrites half of the results
Note how they both go to the same output file -out input1.rRNA.silva.blastout:
The way we name this will have to be changed to distinguish LSU (23S/28S, LSU) and SSU (16S/18S, SSU) ribosomal RNA (rRNA). This will just take some intelligent use of regular expressions.