seqweaver scores

[goutha...@gmail.com]

Hi,

I have a quick question regarding seqweaver. Seqweaver annotates only variants that fall within gene bodies as it requires strand information. I am wondering if it is valid to assign a seqweaver DIS score of 0 for the variants that fall outside of gene bodies ?

I am comparing the credible sets of splicing qtls with non-splicing qtls and most of my non-splicing QTLs falls outside gene bodies. I am wondering if I can I assign a seqweaver DIS of 0 to them as they could not be interrogated and assumed that they would not disrupt the RBP sites.

Thanks,

Goutham A

[Jian Zhou]

Hi Goutham,

As you mentioned, since seqweaver predicts effects on RNA-binding proteins it does not apply to non-gene regions. Whether it is valid to consider it as 0 scores for non-genic regions depends on your specific application though. I would say it is probably safe to assume that a variant outside of genic regions does not have an effect mediated through RNA, but whether it is meaningful to compare seqweaver scores from genic and nongenic regions will depend on your specific purpose.

Best,

Jian