Read the first sequence from fasta file - TFBSTool
0
0
Entering edit mode
HELEN • 0
@ba287559
Last seen 20 months 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 • 763 views
ADD COMMENT

Login before adding your answer.

Traffic: 698 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6