Hello! I am new to single-cell RNASeq and am currently trying to run Kallisto | bustools to make a pseudoalignment. The organism that I work with, Ciona intestinalis is not a model organism, so the files on Ensembl are outdated. I have its genome in FASTA format and a GTF file from collaborators, but I need the cDNA file to run my pipeline. Is there any tool to build a cDNA file from the genome and GTF?
Maybe of interest: Extract sequences from a FASTA file using a gtf file