Short Read Mapping for nt 3 and Above
I am trying to map short reads >=5 nucleotide on a reference genome. The sequences less than 7 are not being mapped with the software's I tried. Is there any mapping tool which can align the sequences with nucleotide 3 and above? I have already used following tools. BWA Bowtie Segemehl Tophat
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Can you elaborate on what you are trying to achieve? Reads of that length are very unlikely to be specific.
WouterDeCoster did not made the comment (yet) but you should not use TopHat anymore ;)
more on topic: have you tried blastn-short or such, I'm guessing that any (NGS) read mapper will have trouble (if possible at all) with mapping those very short reads.
Also curious to know how you got such short reads ...