Question: sequence retrieval in R using fasta file
gravatar for rsabrina93
2.4 years ago by
rsabrina9310 wrote:

I have a Hg19.fasta file and I have a csv file which contains the genomic coordinates of all 23 chromosomes which the sequence is to be retrieved. How can I do it using R?

R sequence retrieval • 1.5k views
ADD COMMENTlink modified 2.4 years ago by Jean-Karim Heriche20k • written 2.4 years ago by rsabrina9310

Not what you ask for, but bedtools getfasta would be the way to do this if you wouldn't constrain to R.

ADD REPLYlink written 2.4 years ago by WouterDeCoster40k
gravatar for Jean-Karim Heriche
2.4 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

You could use the R package seqinr to read the FASTA file with read.fasta(), read the csv file with read.csv() then subset the sequence using the coordinates. There may also be something for you in the Bioconductor GenomicRanges package.

ADD COMMENTlink written 2.4 years ago by Jean-Karim Heriche20k
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