knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-" )
This package provides thermal stable RNA 2ndary structures predicted on full length transcripts mm10 and hg19. The predicted structures are used to filter the bisulfite sequening sites that have potentially incomplete bisulfite conversion on them.
devtools::install_github("ZhenWei10/rBS2ndStructure") library(rBS2ndStructure)
?
to check their documentations.library(GenomicRanges) ?rBS2ndStructure::Struc_hg19 ?rBS2ndStructure::Struc_mm10
rBS_gr = GRanges(seqnames = rBS_df$`#SeqID`, strand = rBS_df$refStrand, ranges = IRanges(start = rBS_df$refPos, width = 1)) rBS_gr_filtered <- rBS_gr[!rBS_gr %over% Struc_hg19]
rBS_2ndStructure_Filter
, the function also helps you mask all the sites on introns and intergenic sequences.rBS_gr = GRanges(seqnames = rBS_df$`#SeqID`, strand = rBS_df$refStrand, ranges = IRanges(start = rBS_df$refPos, width = 1)) rBS_gr$mcols = p.adjust(rBS_df$`p-value_mState`,method = "BH") < .05 rBS_gr_filtered <- rBS_2ndStructure_Filter(rBS_gr,"hg19")
#Extract transcript sequences in fasta files from BSgenome and txdb library(BSgenome.Mmusculus.UCSC.mm10) library(TxDb.Mmusculus.UCSC.mm10.knownGene) txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene tx_seq_extraction(MMusculus,txdb,getwd()) #Run RNAfold in multiple computational clusters RNAfold(1:30,"Small","Fsm") RNAfold(1:30,"Middle","Fmd") RNAfold(1:30,"Large","Flg") # Assemble the predicted transcripts rfold_assembly_tx(txdb,RfdNames = c("Fsm","Fmd","Flg"))
RNAfold
on command line by yourself, the function RNAfold
only works if you implement qsub
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