Support noncoding RNA search with Infernal on Rfam

czbiohub-sf / nf-predictorthologs

*de novo* orthologous gene predictions from bam + bed or fasta/fastq data

MIT License

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Closed olgabot closed 4 years ago

olgabot commented 4 years ago

For these, a few options:

skip the extract_coding step altogether
Take the predicted noncoding reads from extract_coding and search Rfam's fastas: ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/fasta_files/
- search via blast?

olgabot commented 4 years ago