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Old 08-30-2012, 12:48 AM   #1
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Location: Leipzig

Join Date: Oct 2011
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Default bowtie2 local vs. end to end mode


I've made some bowtie2 test to find the best alignment parameters on artificial miRNA sequences. After a few unsatisfactory results, I've tried mapping my reference fasta data to itself.
Is there any explanation why with "end-to-end" mode I've got 100% alignment and with "local" mode only 96%? Shouldn't it be also 100%? These are the same sequences in aligning data and in reference.

Thanks for any response,
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Old 04-18-2013, 02:04 PM   #2
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this is interesting...
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Old 01-30-2014, 10:07 AM   #3
Location: Mc Gill -- Montreal

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In my case, a pair of read align slearly both on chromosome 3 on end to end.
By setting local I have the pair split between 2 chromosmes, I have a better match at a wrong place ..
I feel like I don t get the interest of local alignment except if you don t make a good trimming of you sequences.

My guess for your question is : With local alignment you have several hits when miRNA are close and you finally consider those reads as ambiguous ...
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