Question: Short Read Mapping for nt 3 and Above
gravatar for xeeoff
2.7 years ago by
xeeoff0 wrote:

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

alignment assembly • 627 views
ADD COMMENTlink written 2.7 years ago by xeeoff0

Can you elaborate on what you are trying to achieve? Reads of that length are very unlikely to be specific.

ADD REPLYlink written 2.7 years ago by WouterDeCoster44k

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 ...

ADD REPLYlink written 2.7 years ago by lieven.sterck9.0k
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