Preparing genome and gene annotation

Genome

Genome in a single fastq is required. This is an example of Human GRCh38 genome http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/GRCh38.p13.genome.fa.gz

Matched gene annotation

Matched gene annotation in GTF format (Not GFF format) is needed. The huamn Gencode V34 annotation in GTF format can be found here http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.basic.annotation.gtf.gz.

BWA index of selected genome

A bwa index of selected genome will be built for circular RNA identification using CIRI2. The command used to index genome is: bwa index GRCh38.p13.genome.fa