Hi,
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,
Marta
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,
Marta
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