It seems that most people think Ensembl’s GTF file and cDNA fasta file mean the same transcripts: Watch out! @ensembl's Fasta and GTF annotation files available via do not match (there are transcripts in the GTF not found in the Fasta file. Anyone else expected them to match? — K. Vitting-Seerup (@KVittingSeerup) August 13, 2018 However, my colleagues Joseph Min and Sina Booeshaghi found that for several species, Ensembl’s GTF file and cDNA fasta file do not have the same set of transcripts, so it would not be the same using the cDNA file as opposed to extracting the transcript sequences from the genome with the GTF file for a reference to pseudoalign RNA-seq reads.

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Lambda Moses

Monotheist, Aspie, R lover, advocate for constructive dialogues between science and religion, studying computational biology at Caltech

graduate student

Los Angeles