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2 hours ago by

Netherlands

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.

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2 hours ago
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kees0



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