Read the first sequence from fasta file - TFBSTool
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HELEN • 0
@ba287559
Last seen 9 weeks ago
Greece

Hello, i have this code and i want to put to the subject the first sequence from my fasta file but i don't know how to do it. Thank you

library(TFBSTools)
library(JASPAR2020)
library(Biostrings)
library(S4Vectors)
library(ShortRead)
library(BSgenome.Mmusculus.UCSC.mm10)


fastafile1<- readDNAStringSet("ADAR.Mi_00. (new).20.fa")
readDNAStringSet("ADAR.Mi_00. (new).20.fa")
data(MA0003.2)
data(MA0004.1)
pwmList <- PWMatrixList(MA0003.2=toPWM(MA0003.2), MA0004.1=toPWM(MA0004.1),
                        use.names=TRUE)
readLines("ADAR.Mi_00. (new).20.fa")
subject <- DNAString(".....................")?

SiteSetList <- DNAStringSet(pwmList, subject, seqname="seq1",
                         min.score="60%", strand="*")
head(writeGFF3(SiteSetList))
TFBSTools FASTA RStudio • 84 views
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