Question: Characterize Known And Novel Mirna
0
gravatar for Mushal
7.6 years ago by
Mushal10
Cape Town
Mushal10 wrote:

Hello

I have:

Illumina sequences,50bp,~45M in fastq format

objective:

characterize KNOWN and NOVEL miRNA.

plan:

Align the reads against the reference genome using the bowtie aligner. All reads which align, will blastn against miRBase and Rfam sequences to identify KNOWN miRNAs. The reads which align but not match any known miRNA/RNA sequence will test by Mfold/ RNAfold for hairpin structure to characterize NOVEL miRNAs.

question:

what is the best bowtie parameters to use when annotating miRNA?

any advise to improve the annotation pipeline?

Thank you in advance...

short alignment mirna bowtie small • 2.6k views
ADD COMMENTlink written 7.6 years ago by Mushal10
1
gravatar for Rm
7.6 years ago by
Rm7.9k
Danville, PA
Rm7.9k wrote:

simply use mirdeep2 to acheive all you wanted.

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. http://www.ncbi.nlm.nih.gov/pubmed/21911355

ADD COMMENTlink written 7.6 years ago by Rm7.9k
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