To identify long non-coding RNAs (lncRNAs), I used three computational tools: PLEK, CPAT, and CPC2, to predict lncRNA candidates from a FASTA file. To minimize false positives, I further performed a DIAMOND BLASTx search (using default parameters) against the nr.fasta database. The contigs that showed hits were removed, and the remaining contigs were considered as putative lncRNAs.
However, upon randomly selecting a few sequences from the final lncRNA.fasta file and submitting them to the NCBI BLASTx web server, I observed that some sequences still showed hits. I am unsure how to proceed in such a scenario and would appreciate your guidance on the appropriate steps to refine my lncRNA dataset.
1 answer
You could also use an ORF finder like transdecoder or prodigal as an additional check. Many lncRNAs might have very short ORFs, but are unlikely to have longer ORFs.
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