Question about lncRNA transcript classification

[kasra2018]

Hello,

I'm studying LncRNA and used the noncode database (http://www.noncode.org) for my own study. Unfortunately, there is only a fasta file in this database and no GTF file. While to classify lncRNAs based on the following command, a GTF file is required

FEELnc_classifier.pl -i lncRNA.gtf -a ref_annotation.GTF > lncRNA_classes.txt

so, How can I use the fasta file of this database to create lncRNA classification? Can I add an option in feelnc software to use the fasta file?

[tderrien]

Hi,

Thank you for posting here ;-)

One quick solution would be to align the fasta file on the reference genome using a splice-aware mapper such as minimap2 or STAR.

Hope this helps.