Hi,
Can anyone suggest an aligner which can handle mapping very short reads (<20 bp) to a reference genome?
Thank you.
Hi,
Can anyone suggest an aligner which can handle mapping very short reads (<20 bp) to a reference genome?
Thank you.
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?
I tried SOAP2 and bowtie. SOAP2 could only align reads >30 bp but bowtie did the job beautifully.
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What kind of experiment? RNA-seq? What genome? bacteria ?
What kind of experiment? RNA-seq? Genome ?
And how many reads?