Align to a reversed genome

Question

[marongiu.luigi]

Dear all,

to test the alignment procedure, I inserted a genome in reverse sense into an artificial set of fastq files and aligned against the reference genome in normal orientation. The resulting alignment does not show any mapping.

Is it normal that the aligner could not map the reads because they were in the reverse orientation? I thought that orientation could not affect the alignment procedure...

Thank you

[WouterDeCoster]

I inserted a genome in reverse sense into an artificial set of fastq files and aligned against the reference genome in normal orientation.

Perhaps you could be a bit more specific here, by adding the commands you used?

[marongiu.luigi]

Well, nothing much to add: I reversed the reference fasta file, then used ART to generate the fastq files, then used BWA to align the fatsq to the reference file but there is no alignment. Do you really need all the commands? This is more of a theoretical question...

Answer 1

[ATpoint]

Reference genome orientation of course matters. What is interchangable would be the reference genome in its standard representation and its reverse complement but not its reverse. That would completely ignore that DNA has a 5'->3' polarity that cannot simply be changed at will.

[marongiu.luigi]

OK, though so. Just wanted to be sure. Thanks