MiRdeep2 for paired-end RNA-seq?

Question

[gulamaltab]

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

[Buffo]

In addition to h.mon`s answer it is very unlikely to found mature miRNAs from paired-end reads, the best thing that can happen is found long precursors.

[gulamaltab]

Thank you, I started using Pear yesterday but wasn’t getting matched properly (97% not matched). I thought maybe I’m missing something, atleast now I know we don’t have the option at all. Nevertheless, I thought of aligning my reads with bowtie2 or bwa then convert the Sam file using bwa_sam_converter.pl that should give me the files required for the next step for mirdeep2.

Any suggestion on how to identify novel miRNAs from bwa- stringtie outputs?

Thanks

[GenoMax]

miRNA data generally needs some specific processing (removal adapters etc). Please see instructions for the kit you used and pre-process your data before trying to align it.

Answer 1

[h.mon]

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.

Two suggestions:

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? .