EDGE-pro paired end read input

Hi,

I am running EDGE-pro for prokaryotic RNA seq analysis for differential gene expression.

ccb.jhu.edu/software/EDGE-pro/

I have paired end read data.

The manual states ( ccb.jhu.edu/software/EDGE-pro/MANUAL )

//

*MANDATORY FILES:

-g genome: fasta file containing bacterial genome. If multiple chromosomes/plasmids exist, they must be combined into one file before running EDGE-pro (see “combined multiple files” above)

-p ptt: ptt file with coordinates of coding genes, in Genbank format. If multiple
chromosomes/plasmids exist, see “combine multiple files” above.

-r rnt: rnt file with coordinates of rRNAs and tRNAs, in Genbank format. If multiple chromosomes/plasmids exist, see “combine multiple files” above.

-u reads: fastq file of reads. If multiple fastq files exists, see “multiple reads files” above.

……..

OPTIONAL FILES/PARAMETERS:

-v reads2: fastq file of mates in paired-end data. If this file is not entered, single-end reads are assumed.

-m min: min is an integer value. It is minimum insert size in paired-end library. Default: 0.
-M max: max is an integer value. It is maximum insert size in paired-end library. Default: 500.*
//

so for paired end data should my input look like below ?

/home/ubuntu/EDGE_pro_v1.3.1/EDGE_pro_v1.3.1/edge.pl

-g /home/ubuntu/Desktop/control_fastaq_reads/Reference_files_for_RNA_Seq/file.fna

-p /home/ubuntu/Desktop/control_fastaq_reads/Reference_files_for_RNA_Seq/file.ptt

-r /home/ubuntu/Desktop/control_fastaq_reads/Reference_files_for_RNA_Seq/file.rnt

-u /home/ubuntu/Desktop/control_fastaq_reads/READS_R1.fastq.gz
-v /home/ubuntu/Desktop/control_fastaq_reads/READS_R2.fastq.gz

-o OUTPUTout

-s /home/ubuntu/EDGE_pro_v1.3.1/EDGE_pro_v1.3.1

Thanks

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