Entering edit mode
3.6 years ago
kees
•
0
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:
"NC_000011.10:47350594:CC:C", "NC_000011.10:111908777:C:", "NC_012920.1:8838:G:C", "NC_000001.11:236894530:AA:AAA", "NC_000011.10:2885156:G:GG", "NC_000006.12:7579623:C:",
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.
