tBLASTn v2.7.1+ on the command line: I have a transcriptome as my nucleotide database and I am trying to identify repetitive fragments with translated repetitive queries. I have about ten different repetitive queries I am using, however, for two of them, I get the following error:
"Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options"
I have tried researching online and cannot find a legitimate answer as how to properly bypass this. My output does not contain hits using these two query sequences, however, I know my transcriptome contains them because they are among the most highly expressed transcripts in my transcriptome (I want to fish them out b/c I think they are inflating my TPM values). I have tried "-soft_masking false" but still get the same error. Please help, thanks!