Shifted alignments from Bowtie2

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6.7 years ago

seanb80 • 0

I have some SE100 RNA-Seq data I'm exploring for gene expression by mapping it back to the sequence of a single gene using Bowtie2.

Bowtie2 identifies some valid alignments, but when I view the sorted/indexed bam file, the results seem to almost be shifted one nucleotide to the left from the reference sequence. I used both --very-sensitive-local and --very-sensitive and compared the outputs and they both seem to have this shift visible.

Is this a feature of the program itself, or do I have some misunderstanding of the algorithm or output from the program?

I've attached some IGV images, if that helps visualize the question.

IGV Images

RNA-Seq alignment • 1.4k views

ADD COMMENT • link 6.7 years ago by seanb80 • 0

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Hard to say if those are shifted or just mismapped. Are you sure you are using the exact same reference for mapping and display in IGV?

ADD REPLY • link 6.7 years ago by Brian Bushnell 20k

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