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Old 07-29-2017, 11:13 AM   #1
seanb89
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Location: Seattle

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Default RNA-Seq Bowtie2 alignment shifted left 1 position.

I'm exploring some 100bp SE RNA-seq data using Bowtie2 and a short reference sequence given to me.

When I use the --very-sensitive-local argument in Bowtie2 I get successful mappings, but with a huge number of mismatches. When viewed in IGB/IGV at the nucleotide level, it seems that the mappings are shifted 1 position to the left of the reference.

I've not encountered this before with Bowtie2, and was wondering if this was a feature of the local mapping algorithm, or do I have some other fundamental misunderstanding of the algorithm?
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Old 07-31-2017, 11:15 AM   #2
Brian Bushnell
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Cross-posted here.
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