User: sekawaiwai2006

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Posts by sekawaiwai2006

<prev • 15 results • page 1 of 2 • next >
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question about motif enrichment analysis using PWMenrich
... Hi everyone, i have been working with PWMenrich package to investigate the motifs in promoter sequences. I have a few questions,  first one is about the position of the motifs in the promoter sequences, i am not sure what i am doing is correct or not, here is the code: for( i in 1:length (sum1tar ...
pwmenrich written 15 months ago by sekawaiwai200620
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Comment: C: visualing pwm motif on a DNAstring
... thank you very much for the response, but what i really what to do is plotting these motif on the promoters ( so plotting both the promoter sequence with the motif) because i am interested to see may be just one bp change that exist in these motifs, so i guess the real question is how to plot motif ...
written 20 months ago by sekawaiwai200620
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visualing pwm motif on a DNAstring
... Hi everyone,  so i have been doing analysis on promoters , SL_promoter_stringset is a list of 1600 promters stringsets, MotifList are a list of pfm for around 100 motifs, namely 'M0006_1.02 ' etc i am going to see if these motifs are part of the promoters here is my code dllm4<-makePriors(S ...
pwmenrich dnastringset written 20 months ago by sekawaiwai200620 • updated 20 months ago by Robert Stojnic50
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Comment: C: problem creating txdb object and bsgenome for solanum pennellii
... Thank you so much, it works now! ...
written 21 months ago by sekawaiwai200620
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Comment: C: problem creating txdb object and bsgenome for solanum pennellii
... Thank you so much, it works now! ...
written 21 months ago by sekawaiwai200620
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Comment: C: problem creating txdb object and bsgenome for solanum pennellii
... Hi Martin , thank you so much for your response, everything works except for the last step > getSeq(twob,p) Error in .local(con, format, text, ...) : UCSC library operation failed In addition: Warning message: In .local(con, format, text, ...) : NC_028637.1 is not in GCF_001406875.1_SPENNV20 ...
written 21 months ago by sekawaiwai200620
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problem creating txdb object and bsgenome for solanum pennellii
... Hi everyone, so i am trying to extract the 1000bp upstream, for every gene in solanum pennellii, i know i would need to build the txdb object and the bsgenome for this, firstly i downloaded the fasta format genome and the gff file from ncbi genome database http://www.ncbi.nlm.nih.gov/genome/?term= ...
bsgenome promoter txdb written 21 months ago by sekawaiwai200620 • updated 21 months ago by Martin Morgan ♦♦ 20k
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Comment: C: extracting promoter region error for A.thaliana
... so i have changed the code now  library("TxDb.Athaliana.BioMart.plantsmart28") txdb <- TxDb.Athaliana.BioMart.plantsmart28 library("BSgenome.Athaliana.TAIR.TAIR9") genome<-BSgenome.Athaliana.TAIR.TAIR9 gn <- sort(genes(txdb)) up1000 <- flank(gn, width=1000) up1000seqs <- getSeq(ge ...
written 22 months ago by sekawaiwai200620 • updated 22 months ago by Martin Morgan ♦♦ 20k
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extracting promoter region error for A.thaliana
... Hello  Below are the codes that i used in order extract the upstream 1000 bp for every genes in A.thaliana. however, i get an error at the end when using the command :up1000seqs <- getSeq(genome, up1000), does anyone know what is the problem here??  thx Error in (function (classes, fdef, mtab ...
txdb promoter region written 22 months ago by sekawaiwai200620 • updated 22 months ago by Martin Morgan ♦♦ 20k
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Comment: C: error making txdb object from gtf file
... hi michael , thx for the reply, however i got another error trying to run it like this txdb <- makeTxDbFromGFF(gtffile) ERROR Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... Error in .merge_transcript_parts(tra ...
written 22 months ago by sekawaiwai200620

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