config.yaml

# CircOrf-config-file
# This configuration file includes all adjustable options and files for CircOrf.
# Please input full absolute path.
# You can submit your question by submitting issue on github or sending an e-mail
# E-mail = mr1997@snnu.edu.cn
# Date = 30 July 2021

#################
# required data #
#################

# The path of genome file
transcript_fasta: ./test_data/test_transcript_human_GRCh38.fa

# The path of ribo-seq raw reads file(single)
raw_reads: 
           - ./test_data/test.fastq

# The path of ribosome sequence file
ribosome_fasta: ./test_data/test_rRNA_human.fa

# The path of Candidate circRNA
circrnas: ./test_data/test_circRNA.fa

# The path of gtf file of circRNA, the file should be generated in our way(README.md) 
circrna_gtf: ./test_data/test_circRNA.txt

#####################
# Required location #
#####################

# The path of folder for storing the final result
result_file_location: ./result

# The path of folder for storing temporary results
tmp_file_location: ./tmp

#################
# OTHER OPTIONS #
#################

# The thread to run bowtie or STAR
thread: 12

# type of Ribo-seq data, value: sra or fastq
ribotype: fastq