Table 2. Open in new tab The description...

Parameters

Description

—ref_gtf/-r <string>

Combined transcriptome assembled by different tools in GTF format (just combine the different assemblies into a GTF file, combine.gtf)

—ref_genome/-g <string>

Reference genome in FASTA format;

—bam/-b <string>

BAM file;

—strand/-s <string>

—min_cov/-c <float>

Min coverage of recovered transcripts, default: 1;

—output/-o <string>

Output path, default: ./TransBorrow_results/TransBorrow.gtf;

—min_trans_len/-l <int>

Min length of recovered transcripts, default: 200;

—cre_num/-n <int>

Credible sub_paths assembled by at least this number of tools, default: 2;

—min_seed/-d <float>

Min seed coverage for extension, default: 0;

—temp_dir/-T <string>

Directory storing temporary files, default: ./TransBorrow_tmp;

—threads/-t <int>

Number of threads to launch, default: 1;

—version/-v

Show current version of TransBorrow;

—help/-h

help infomation;

Table 2.

The description of TransBorrow’s parameters.

Parameters	Description
—ref_gtf/-r <string>	Combined transcriptome assembled by different tools in GTF format (just combine the different assemblies into a GTF file, combine.gtf)
—ref_genome/-g <string>	Reference genome in FASTA format;
—bam/-b <string>	BAM file;
—strand/-s <string>	Strand-specific RNA-Seq reads orientation. If reads are paired: 1) Use <unstranded> to indicate RNA-seq reads are nonstrand-specific; 2) Use <first> to indicate fr-first-stranded RNA-seq read; 3) Use <second> to indicate fr-second-stranded RNA-seq reads; If reads are single: 1) Use <single_unstranded> to indicate RNA-seq reads are nonstrand-specific; 2) Use <single_forward> to indicate RNA-seq reads forward; 3) Use <single_reverse> to indicate RNA-seq reads reverse;
—min_cov/-c <float>	Min coverage of recovered transcripts, default: 1;
—output/-o <string>	Output path, default: ./TransBorrow_results/TransBorrow.gtf;
—min_trans_len/-l <int>	Min length of recovered transcripts, default: 200;
—cre_num/-n <int>	Credible sub_paths assembled by at least this number of tools, default: 2;
—min_seed/-d <float>	Min seed coverage for extension, default: 0;
—temp_dir/-T <string>	Directory storing temporary files, default: ./TransBorrow_tmp;
—threads/-t <int>	Number of threads to launch, default: 1;
—version/-v	Show current version of TransBorrow;
—help/-h	help infomation;

Parameters	Description
—ref_gtf/-r <string>	Combined transcriptome assembled by different tools in GTF format (just combine the different assemblies into a GTF file, combine.gtf)
—ref_genome/-g <string>	Reference genome in FASTA format;
—bam/-b <string>	BAM file;
—strand/-s <string>	Strand-specific RNA-Seq reads orientation. If reads are paired: 1) Use <unstranded> to indicate RNA-seq reads are nonstrand-specific; 2) Use <first> to indicate fr-first-stranded RNA-seq read; 3) Use <second> to indicate fr-second-stranded RNA-seq reads; If reads are single: 1) Use <single_unstranded> to indicate RNA-seq reads are nonstrand-specific; 2) Use <single_forward> to indicate RNA-seq reads forward; 3) Use <single_reverse> to indicate RNA-seq reads reverse;
—min_cov/-c <float>	Min coverage of recovered transcripts, default: 1;
—output/-o <string>	Output path, default: ./TransBorrow_results/TransBorrow.gtf;
—min_trans_len/-l <int>	Min length of recovered transcripts, default: 200;
—cre_num/-n <int>	Credible sub_paths assembled by at least this number of tools, default: 2;
—min_seed/-d <float>	Min seed coverage for extension, default: 0;
—temp_dir/-T <string>	Directory storing temporary files, default: ./TransBorrow_tmp;
—threads/-t <int>	Number of threads to launch, default: 1;
—version/-v	Show current version of TransBorrow;
—help/-h	help infomation;