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Sortmerna: index fna file from ncbi

Hello,

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!

sortmerna index rrna
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updated by GenoMax GenoMax • written by Stella • Stella

1 answer

Take a look at indexdb_rna -h command help to see how you can do that.

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written by GenoMax GenoMax

I don't see some other option on indexing... I have used the standard command of --ref .fasta,db.idx

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written by Stella • Stella

You should be able to replace the input fasta with one you want to use. .fna is NCBI's fasta file designation.

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written by GenoMax GenoMax

Ok, thank you. I will try running it even if the file seems empty.

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written by Stella • Stella

No that would not help. You should figure out why the index files are empty. Perhaps sortmeRNA requires the extension to be .fasta etc.

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written by GenoMax GenoMax

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