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Question: Mirna Prediction from mirbase database
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gravatar for bioz
21 months ago by
bioz • 20
bioz • 20 wrote:

Hai Stars, I want to identify known and conserved miRNAs from my data. For that i trimmed my reads (fastq Paired end) based on the length: 16bp minimum and maximum of 36 bp. For conserved miRNA identification i downloaded mirbase matured miRNA and i did homology search. But i didn't get any results because mirbase data base contains "U" base and which is not in my read.How to alignment when reference has "U" base instead of "T"

sequencing rna-seq next-gen • 429 views
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modified 21 months ago by Buffo • 1.8k • written 21 months ago by bioz • 20

I also tried to change "U" to "T" from reference but i dint get any alignment percentage.Which aligner i can trust ?

ADD REPLY • link written 21 months ago by bioz • 20
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gravatar for Buffo
21 months ago by
Buffo • 1.8k
Buffo • 1.8k wrote:

I recommend you Bowtie, but also, I recommend you map your reads against the entire genome and then count the read that maps to the known mirnas by using the gff3 of mirbase. If you map your reads to the fasta containing mirna sequences you will get biased results since there are some redundant miRNAs (mainly in mouse).

ADD COMMENT • link written 21 months ago by Buffo • 1.8k
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