For a list of mutations in SPDI format, I would like to fetch the flanking sequences, in order to idenitfy near sites that can be targeted with Crispr-Cas
The main issue is that in the list of SPDI identifiers is based on multiple different genome alignments.
Here is an example:
I have tried the rentrez package, but couldn't find a way to only download a particular fraction of the sequences.
Would appreciate any suggestions on how to approach this, including R-based approaches or using galaxy.