config.yaml

# #######   CircCode-cofig-file   #######
# This configuration file includes all possible options and files for CircCode.
# Please input full path as well as for running all process.
# You can submit your question by submitting issue on github or sending an e-mail

# Version = 1.0
# E-mail = sps@snnu.edu.cn
# Date = 20 July 2019

# The name of genome
genome_name: virGenome

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

# The path of genome file
genome_fasta: /full/path/to/genome/file.fa

# The path of gtf file of genome
genome_gtf: /full/path/to/gff/file.gff

# The path of ribo-seq raw reads file
raw_reads:
           - /full/path/to/raw/reads_1.sra
           - /full/path/to/raw/reads_2.sra

# The path of ribosome sequence file
ribosome_fasta: /full/path/to/rRNA/file.fa

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

# The path of Candidate circRNA
circrnas: /full/path/to/Candidate/circRNA.fa

# The path of adapters file
riboseq_adapters: /full/path/to/riboseq-adapters.fa

# Coding sequence
coding_seq: /full/path/to/coding_sequence.fa

# Non-coding sequence
non_coding_seq: /full/path/to/non_coding_sequence.fa

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

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

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

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

# The type of reads, please input single or pair
reads_type: single

# Coverage counts, DEFAULT = 10.
coverage_counts: 10

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

# merge all the NGS data: T or F
merge: F

# Weather classify the sequences by BASiNET: T or F
classify: T

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