How do I get a gtf file to use rnaQUAST

Question

[kristina.mahan]

I want to run rnaQUAST on my transcriptome assembly on a yellow green algae. rnaQUAST says it needs a transcripts fasta file, genome assembly fasta file, and a gene coordinates gtf file from Ensembl or Gencode. Do I just try to find the closest related organism to my organism or how do I go about this?

python rnaQUAST.py \ --transcripts /PATH/TO/transcripts1.fasta /PATH/TO/ANOTHER/transcripts2.fasta [...] \ --reference /PATH/TO/reference_genome.fasta --gtf /PATH/TO/gene_coordinates.gtf

Answer 1

[Shraddha]

I have a similar issue, since the annotation for my species isn't reliable. Using a closely related organism works well, but you may want to add checks to see how much data you lost due to using a different organism.