All you need is:
1) Transcriptome (equivalent of transcriptome #FASTA file)
2) Gene annotations (equivalent of #GTF/#GFF file)
3) RNAseq reads (your #FASTQ file)

#BgeeCall will handle the rest and will let you know if a gene is present or absent!

❓ And what if your species is not present in this database? What do you do then?
❓ Isn't it enough to decide on an arbitrary cutoff (e.g. TPM < 1) for expression?

👉 Actually, you can do better than that. How? #BgeeCall #R package:

www.bioconductor.org/packages/rel...