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Old 09-29-2015, 01:07 PM   #1
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Default Bowtie alignments and --local function

I've just starting sequencing using MiSeq and am stumbling a bit in the analysis of my output reads, specifically using bowtie2 to align the reads to the reference genome. I'm using bowtie to get a rough estimate of what my amplification looks like and it's generally intuitive and quick. However:

When aligning reads to a genome sequence, what is “% reads align exactly 1 time” vs “% reads align >1 times” in the output? From my understanding, bowtie only records the best possible match (by default).
Is this saying that, to use an example from one of my samples, 40.26% of my reads align equally well to several places in the genome, suggesting a repeat region, while only 17.35% of my reads align to a unique region?
Or should this be interpreted as 40% of the reads align somewhere in the genome that already has one or more reads assembled to it, and that 17% of my reads are “unique”?

Also, my —-local alignments are substantially different (99% of reads align using —-local while only <70% without) from those where I do not specify —-local, even though I trim adapters and low quality reads before aligning (using trimmomatic). From my understanding of —-local, it should give a slightly more liberal alignment, but the two should be closer especially with trimming beforehand.

Forgive my ignorance and thanks for any advice.

aberry814 is offline   Reply With Quote

bowtie, genome alignment, genome amplification, miseq

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