Hi, I'm new to RNAseq data analysis, I've miRNA seq paired-end data, I would like to use mirdeep2 to identify novel miRNAs but I can’t seem to find the option to input both R1 and R2 fastq files. How do I input both files? Any help would be great. Thanks
There is no option to input R1 and R2 fastq files because probably miRDeep2 author considered very unlikely someone would do paired-end sequencing for miRNA.
All reads should overlap, use some paired-end read merger (like BBMerge, PEAR or FLASH), and discard pairs that do not merge.
Or use just the R1 fastq file.
See previous discussion at single- or pair-end small RNA seq for miRNAs? .