Hello everybody,
I started to use Bioconductor package TFBStools in R because I was looking for the 2014 version of JASPAR database
to have a list of putative TF on a fasta sequence.
I used MAPPER2 serach engine but is related to an old version of that database.
I would like to ask you how can I put my fasta sequence in that database.
Thank you for the attention
Alessio
P.s I'm not a bioinformatician and I never used R, I'm learning it on my own XD
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written
by
alessio.stevano •
1 answer
Do you need help with getting the FASTA sequence to work with TFBStools? If you are working with hg19 then I think you can use the bioconductor library BSgenome.Hsapiens.UCSC.hg19 to retrieve the genome & sequence from a specific region like this:
library(BSgenome.Hsapiens.UCSC.hg19)
genome <- BSgenome.Hsapiens.UCSC.hg19
seq <- getSeq(genome, "chr12", start = 6643585, end = 6647537, strand = '+')
Pardon me if I misunderstood your question. I just took cues from the tags you used.
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written
by
komal.rathi
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