Is there any alternative ways to set identity and e-vlaue for bowtie2 mapping?

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7.5 years ago

biofuture.jiang • 0

Dear all

The MetaPhlAn2 use bowtie2 to align metagenomics reads to clade specific marker genes so that the speed is very fast. However, we do not know whether the very sensitive option for bowtie2 is too stringent or not. When using bowtie2 to map metagenomics reads to genes, whether it is possible to get an identity value or e-value for each mapped reads. The bowtie2 indeed have some parameters for alignment like gap penalty, gap extending and mismatch, but there is no way to evaluate the alignment quality for every mapped reads. Thanks

alignment sequence • 1.6k views

ADD COMMENT • link 7.5 years ago by biofuture.jiang • 0

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The MAPQs don't suffice for this? Or are you outputting all alignments, in which case the MAPQ isn't informative?

ADD REPLY • link 7.5 years ago by Devon Ryan 104k

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