What are the input files for CeleScope?Home FAQ Bioinformatics CeleScope What are the input files for CeleScope?The input files for CeleScope are:Sequencing FASTQ files.Reference genome FASTA file.Reference genome annotation GTF file.The fasta and gtf files need to be indexed beforehand as mentioned on the CeleScope GitHub page. Please be aware that due to the overhaul of the CeleScope code base, if you have recently upgraded from v.1.x to v.2.x, you will need to reindex your reference fasta and gtf files before using CeleScope for the first time.