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Old 04-21-2009, 10:57 AM   #1
AnamikaDarwin
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Question Helicos

Hello,

Is it possible to use MAQ for helicos reads?

Thanks,
Anamika
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Old 04-21-2009, 12:00 PM   #2
lh3
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I think BWA would be better as MAQ does not do gapped alignment for single-end reads while short deletion is the major error for helicos reads. But if you use BWA, you need to change the default settings. I have never tried helicos reads and so cannot say what is the best.
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Old 04-21-2009, 01:57 PM   #3
Chipper
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When I tried it bowtie worked well but without gaps, don't know if that has been updated. bwa was not available them, if it allows deletions it should be even better. ZOOM! is also an option that does gapped alignments.

Would be nice to get some real Helicos data...
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Old 06-12-2009, 03:15 PM   #4
AnamikaDarwin
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Quote:
Originally Posted by lh3 View Post
I think BWA would be better as MAQ does not do gapped alignment for single-end reads while short deletion is the major error for helicos reads. But if you use BWA, you need to change the default settings. I have never tried helicos reads and so cannot say what is the best.




Hello Heng,

I took your advice on using BWA for helicos data. Since helicos does not have inherent quality scores associated with it, I simulated and gave "perfect" scores for all the reads. In the downstream analysis, I realize the read depth of the alignments is very low. Is this a result of the simulated qual scores? Do you have suggestions on flags that I can tweak to get better alignments?

Thanks,
Mika
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Old 06-12-2009, 10:45 PM   #5
Chipper
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What settings did you use for gaps? Perhaps lowering the penalty would help.
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Old 06-13-2009, 03:01 PM   #6
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Quote:
Originally Posted by Chipper View Post
What settings did you use for gaps? Perhaps lowering the penalty would help.


Hi Chipper,

I changed the default values for all the gap parameters -o, -O & -E. I get marginally more alignments, but still the depth is quite low.

~ Mika
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