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Old 07-14-2011, 08:35 PM   #1
hclee
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Default Mapping very short (<20 bp) reads

Hi,

I've been a SOAP2 user but recently got some very short reads (<20 bp) to map to a reference genome. Can someone please suggest an aligner which can handle the problem? SOAP seems to map only reads >30 bp.

Thank you.
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Old 07-14-2011, 09:25 PM   #2
Kennels
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Quote:
Originally Posted by hclee View Post
Hi,

I've been a SOAP2 user but recently got some very short reads (<20 bp) to map to a reference genome. Can someone please suggest an aligner which can handle the problem? SOAP seems to map only reads >30 bp.

Thank you.
You could try bowtie or bwa
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Old 07-15-2011, 08:36 AM   #3
sdarko
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Command-line BLAST could work well.
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Old 07-15-2011, 08:48 AM   #4
husamia
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I am curious about your data and brings unrelated question? Aren't <20bp reads considered ambigous? Technically its possible that good amount of your reads align to multiple regions in genome. Hence (ambiguous). Is there data to support what is a good enough read length that provides least amount of ambiguous-ness?
I was playing around with searching and as long as I enter random sequence shorter than 20bps in general I get multiple perfect match with genome.

Last edited by husamia; 07-15-2011 at 08:51 AM.
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Old 07-15-2011, 08:53 AM   #5
mnkyboy
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Originally Posted by husamia View Post
I am curious about your data and brings unrelated question? Aren't <20bp reads considered ambigous? Technically its possible that good amount of your reads align to multiple regions in genome. Hence (ambiguous). Is there data to support what is a good enough read length that provides least amount of ambiguous-ness?
I was playing around with searching and as long as I enter random sequence shorter than 20bps in general I get multiple perfect match with genome.
I was wondering about this too. Shorter than 20 you cannot differentiate them from random sequences.
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