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: /full/absolute/path

# The path of ribo-seq raw reads file(single)
raw_reads: 
           - /full/absolute/path

# The path of ribosome sequence file
ribosome_fasta: /full/absolute/path

# The path of Candidate circRNA
circrnas: /full/absolute/path

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

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

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

# The path of folder for storing temporary results
tmp_file_location: /full/absolute/path

################################
# Adjustable filter parameters #
################################

# The thread to run tophat2 and SEPCtr, DEFAULT = 6
thread: 12

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

# The path of trimmomatic.jar
trimmomatic_jar: ./requiredSoft/trimmomatic-0.38.jar

# The path of your train_pos.fa for M6A, DEFAULT = default_path
pos_fa: default_path

# The path of your train_neg.fa for M6A, DEFAULT = default_path
neg_fa: default_path

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