Question: MiRdeep2 for paired-end RNA-seq?
gravatar for gulamaltab
11 months ago by
gulamaltab0 wrote:

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

ADD COMMENTlink modified 11 months ago • written 11 months ago by gulamaltab0

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.

ADD REPLYlink written 11 months ago by Buffo1.8k

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 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?


ADD REPLYlink written 11 months ago by gulamaltab0

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.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax78k
gravatar for h.mon
11 months ago by
h.mon29k wrote:

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? .

ADD COMMENTlink written 11 months ago by h.mon29k
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