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Mapping Very Short (<20 Bp) Reads

Hi,

Can anyone suggest an aligner which can handle mapping very short reads (<20 bp) to a reference genome?

Thank you.

short aligner
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written by Hcl • Hcl

What kind of experiment? RNA-seq? Genome ?

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written by Pasta • Pasta

What kind of experiment? RNA-seq? What genome? bacteria ?

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written by Pasta • Pasta

And how many reads?

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written by Fred Fred

2 answers

I think you can use any of the short reads aligners. Just be careful to set number of mismatches to 0 or 1 and maybe disable indels, as @ 20bp sequence length the probability of random match is quite high. That depends of course on the size of your genome.
What is your reference genome size?

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written by Leszek Leszek

yes try bowtie with -v 0 parameter to set the number of mismatches to 0

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written by Nicolas Rosewick Nicolas Rosewick

I tried SOAP2 and bowtie. SOAP2 could only align reads >30 bp but bowtie did the job beautifully.

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written by Hcl • Hcl

I'm using GEM-mapper for most aplications - give it a try:)

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written by Leszek Leszek

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