miRNA homology search

Question

[seta]

Hi all,

I have miRNA reads that comes from Illumina, and 22-24 in length after trimming. I want to do homology search using mirbase or what you suggest me for differentially expressed reads in my experiment.

In the case of mirbase, could you please advise me whether I should do blast against "mature sequence" or "stem-loop sequence (precursor)"? Another question is about miRNA ontology, we have for example "DAVID" for coding sequences. What tool you recommend me to do miRNA ontology? Any comments and experience is welcomed and appreciated.

[seta]

No any comments and idea

Answer 1

[Chirag Nepal]

IF you have unmapped sequence from illumina, you should begin by mapping those sequence reads to the genome.

You could use either BWA/Bowtie to map it to the genome. Once the reads are mapped to the genome, you can do read-counts from your libraries on known mirna, which will give you diff expressed genes. Then you can continue other downstream analysis, but first you need to map those reads and have either SAM/BAM file.

[seta]

Thanks for your reply Chirag. I used clc genomics workbench software to perform expression analysis and collected differentially expressed reads. My question is about the blast and annotation of these differential reads.

[seta]

Thanks for your reply Chirag. I used clc genomics workbench software to perform expression analysis and collected differentially expressed reads. My question is about the blast and annotation of these differential reads.