Question: tBLASTn - 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
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gravatar for molly77
5 days ago by
molly7710
molly7710 wrote:

Hi,

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!

ADD COMMENTlink written 5 days ago by molly7710

The error seems pretty self-explanatory to me. What is in the query sequence that is causing problems? Any non-standard characters?

ADD REPLYlink written 5 days ago by Mensur Dlakic2.4k

No non-standard characters, I have already troubleshooted for that. I believe it's because its highly repetitive (a Google search of the exact error message hints that it's because it's repetitive, but provides no other information).

ADD REPLYlink written 4 days ago by molly7710
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