I am working with miRNAs in tea, and for finding out conserved and novel miRNAs, I have blasted the filtered data set of sRNA sequences against the miRBase. But the output only shows the aligned reads and is a very large file. So how can i get the results of non-aligned reads that will give me the putative novel miRNAs?
Hi Debasish,
I suggest you to use either miRge 2.0 (PMID: 30153801) or miRDeep2 (PMID: 2191135). Both the tools are specifically tailored for miRNA profiling. And both of them will help to identify unaligned reads and novel miRNAs. Both the tools are easily accessible and very user friendly provided you have basic knowledge of Linux.
Or you can find these tools on GALAXY and analyze data online if you are not well versed with Linux OS.
There are multiple published articles available online that have used the aforementioned tools. I suggest you to use them to set your pipeline, replicate any of the relevant study to make sure you are going in right direction and employ same pipeline on your dataset as well.
All the best.
Thank You Krishna Patel ji. But can the miRDeep2 tool be used if dont have the genome sequence of my sample. I only have the small RNA seq data and i want to test it against the miRBase mature sequences.
You can use genome of closest organism if you don't have genome of the organism of your interest.
Krishna Patel can you please send me the link of downloading mirdeep 2?
Following is the link to paper:
https://academic.oup.com/nar/article/40/1/37/1275937
Following is link to download tool:
https://github.com/rajewsky-lab/mirdeep2
All the best.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Nucleic Acids
- RNA
- Small RNA
- microRNA