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How to align miRNA seq data to known miRNAs?

Hello.

I tried to align miRNA seq data to mirBase mature and hairpin RNAs with bowtie and bowtie2 and got very low alignment. I tried some experiments aligning sequences from reference file and it seems that the problem is that mature mirnas from mirBAse are 5>3 RNAs while my Reads are 3>5 cDNAs. Could this be a problem? If it is, building index from mature.gff3 file could help, however i cannot find how to do it.

Thanks.

next-gen rna-seq alignment
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written by linaskunigenas • linaskunigenas

Did you try to match to both strands (usually the default) or just the forward? Try BLAT of some unmapped reads.

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written by Asaf Asaf

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