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Old 09-04-2015, 07:15 AM   #1
Irina Pulyakhina
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Location: Oxford

Join Date: Sep 2010
Posts: 24
Default almost no hits when mapping against miRBase

Hi guys,

I'm trying to map human miRNA data (Illumina 2500, ~22bp reads, adapters already trimmed) to the most recent release of microRNA database, miRBase (hairpin miRNA and mature miRNA). I'm using bowtie, -l 8 and the rest of the options are default.

I find only 0.5% of my data mapped to human mature miRNAs and 2.5% of my data mapped to hairpin miRNA... I rerun it for publicly available miRNAs (five random samples, and I removed adapters for those as well, so the data is potentially clean) and I reproduce similar numbers -- around 5% of reads map to hairpin miRNAs and < 1% of reads map to mature miRNAs. I guess this means that something is wrong with my database and not the samples...

To index miRBase datasets, I just used standard `bowtie build` command without any specifics. Am I doing it wrong and should I use some special parameters when indexing a large set of short sequences? Does anyone have any experience with this? People working with miRNA sequencing data, how do you index miRBase before you map your data to it?

Thank you all very much in advance!

Cheers,
Irina
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