Mapping Very Short (<20 Bp) Reads

Question

[Hcl]

Hi,

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

Thank you.

[Pasta]

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

[Pasta]

What kind of experiment? RNA-seq? Genome ?

[Fred]

And how many reads?

Answer 1

[Leszek]

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?

[Nicolas Rosewick]

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

Answer 2

[Hcl]

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

[Leszek]

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