I have a fasta file I am planning to use to make a kallisto index. I would like to filter it and remove anything with gene_biotype and transcript_biotype that is rRNA.
I tried to import my fasta file in R using read.fasta however it becomes a list and I cannot filter the file. Is there an easy way to filter the file? Ensembldb seems very useful however I do not want to download the file from Ensembl. I want to import the file that I already have because I have merged the cDNA and ncrna from Ensembl and then use the new file to make a kallisto index.