Should I Use Strand Info, When I Overlap Snps With Genes ?

Question

[biorepine]

I would like to overlap my SNPs with gene bodies. For this do I need to overlap based on their strand direction ?

Thanx in advance

Answer 1

[Sean Davis]

A SNP will affect a gene on either strand since a SNV on the forward strand will have a change on the reverse strand (the complement) as well, so for the purposes of overlaps, the strand is unimportant. For determining the effect of the SNV on the coding sequence, you may need to complement the base.

[biorepine]

I was trying to overlap a SNV (anti-sense) with a region, where it is shared by a coding gene (sense) and a lncRNA gene (anti-sense). So based on your suggestion, SNV should belong to coding gene but not lncRNA gene ?

[Ryan Thompson]

Any kind of nucleotide variation in double-stranded DNA must affect the sequence of both strands. Any gene that overlaps the SNV's coordinate will have its sequence affected. The only relevance of the SNV stand orientation is in deciding whether to use the base or its complement.

[biorepine]

Thanx for the nice explanation but what about the region that produce both coding and noncoding RNA ? To which transcript do you assign the SNV ?

[Sean Davis]

The strand is unimportant for "overlaps" so the SNV would overlap all transcripts that share a base with that SNV, regardless of strand.