Insert a fasta sequence into TFBStools under R environment
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Entering edit mode
7.0 years ago

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

 

 

 

 

R sequence genome • 1.3k views
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Entering edit mode
7.0 years ago
komal.rathi ★ 4.0k

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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