Single Copy lncRNA

Question

[Kutti]

From a study i got a set of lncRNAs. How can i find out the single-copy lncRNAs? Which tool can I use?

Answer 1

[Semir]

I think you should be able to use Blast

# Create BLAST database
makeblastdb \
    -in ${input_fasta} \
    -dbtype nucl \
    -parse_seqids \
    -out lncrna_db

# Perform all-vs-all BLAST search
blastn \
    -task megablast \
    -query ${input_fasta} \
    -db lncrna_db \
    -evalue ${params.evalue} \
    -num_threads ${task.cpus} \
    -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore" \
    -max_target_seqs 5 \
    -out blast_results.tsv

At which point you can then filter the output tsv for single-copy lncRNAs.

I generated this answer using amplicon.ai, a tool I've been building to iteratively write and execute pipelines easier. Feel free to try it out

[Kutti]

Thank you so much for the replay. I did the blast search but, all lncRNA sequences are showing more than 1 hits. So i ws confused. Does the result shows that there are no single copy lncRNA?

I will surely try it out 'amplicon.ai'