after running the rrna removal on my rnaseq samples I saw that I have some overpresented sequences in one of them. By blasting, I saw that they are rrna but from subunits 45s,40s,48s,5.8s. As these are not included in the sortmerna database and my sequences were not compared against them, they were left over and that sample is a major outlier.
Is it possible to index fna files that contain the sequences for these other subunits downloaded from ncbi and rerun the removal including them? I haven't succeded with the normal function (.stats file is few bytes big).
Many thanks in advance!