I am running EDGE-pro for prokaryotic RNA seq analysis for differential gene expression.
I have paired end read data.
The manual states ( ccb.jhu.edu/software/EDGE-pro/MANUAL )
-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.
-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 ?
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