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15 days ago
Kutti
•
0
From a study i got a set of lncRNAs. How can i find out the single-copy lncRNAs? Which tool can I use?
From a study i got a set of lncRNAs. How can i find out the single-copy lncRNAs? Which tool can I use?
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
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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'