I am trying to do in silico digestion of cotton reference genome using SimRAD package in R, but I kept getting error message:
Error in strsplit(DNAseq, split = recognition_code, fixed = FALSE, perl = FALSE) :
non-character argument
My codes are as follows:
simseq
Dear Hui Fang ,
Look the link, may be useful.
https://cran.r-project.org/web/packages/SimRAD/SimRAD.pdf
http://insilico.ehu.es/digest/
Regards, Shafagat
Hi Dr. Mahmudova,
Thank you very much for the links. However, neither of the tools were working for my case. SimRAD can't handle the big genome as mine (cotton reference genome, about 2.4 Gb unzipped). The webpage of the second link doesn't have the genome I am working on (Gossypium hirsutum).
Anyway, thank you for the information.
Best regards,
Hui
Did you check this question linked below?
You also have the option with the Biostrings package (link below too)
Also, try to install EMBOSS locally and check on the REBASE options
https://www.researchgate.net/post/Does_anyone_know_of_a_program_that_can_do_insilico_genome_restriction_enzyme_digest
https://www.r-bloggers.com/restriction-digestion-of-eukaryotic-genomes-in-r/
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